Fixing Our Pakistan Problem

By Daveed Gartenstein-Ross
Journal of International Security Affairs
Spring 2009

A deadly suicide bombing hit India’s embassy in Kabul on July 7, 2008. After the U.S. learned that the attack may have implicated rogue elements of Pakistan’s powerful Inter-Services Intelligence agency (ISI), American strategic planners decided that the U.S. needed to deliver a stern warning to Pakistan. Late that month, CIA deputy director Stephen R. Kappes secretly traveled to Islamabad to present Pakistani officials with information about the ISI’s ties to extremists in the country’s tribal areas. The New York Times opined that this was “the bluntest American warning to Pakistan since shortly after the Sept. 11 attacks about the ties between the spy service and Islamic militants.”1

Pakistan is one of the critical countries in America’s “war on terror.”2 After the October 2001 U.S. invasion of Afghanistan toppled the Taliban, most of al-Qaeda’s senior leadership relocated to Pakistan’s federally administered tribal areas, the mountainous region that borders Afghanistan. Once there, the terrorist leaders set about finding allies within tribal society. Though Pakistan’s military mounted a campaign to flush out al-Qaeda after the group was connected to multiple assassination attempts against then-president of Pakistan Pervez Musharraf, the military suffered so many losses that Musharraf eventually concluded he had no option but to negotiate with his would-be killers. In March and September 2006 he consummated both halves of the Waziristan accords, peace agreements that essentially ceded Waziristan to Islamic militants. Those accords, and other agreements that Pakistan’s government has entered since, have helped al-Qaeda establish a new safe haven in Pakistan.

Just as Pakistan is critical to the war on terror, American analysts increasingly believe that support for religious militancy within the country’s ISI and military is one of the key obstacles to formulating a sound Pa-kistan policy. It is important that policymakers and scholars understand how support for religious militancy has gained a foothold in Pakistan’s ISI and military, and the problems that it now poses.

Practical in form, Islamist in function

At their founding, Pakistan’s military and intelligence services were shaped by the country’s colonial experience. The ISI was formed by a British army officer, Major General R. Cawthome, in 1948. Originally the agency was charged with coordinating the intelligence functions of Pa-kistan’s army, navy, and air force, and “confined itself to playing its specified role.”3

Shuja Nawaz notes that Pakistan’s army had an elitist orientation at the outset. “The senior echelons were still British officers who had opted to stay on,” he writes, “and they were in turn succeeded by their native clones, men who saw the army as a unique institution, separate and apart from the rest of civil society and authority.”4 Despite this, Husain Haqqani, who is currently Pakistan’s ambassador to the U.S., has written that the later Islamization of Pakistan’s military was “not just the inadvertent outcome of decisions by some governments,” such as that of General Muhammad Zia ul-Haq. Rather, since Pakistan’s formation, its leaders “have played upon religious sentiment as an instrument of strengthening Pakistan’s identity,” and tried to “manage” Islamic militancy “so that it serves its nation-building function without destabilizing internal politics.” Thus, later Islamization policies were, in Haqqani’s view, “the extension of a consistent state ideology, not an aberration.”5 One example is the early fighting between Pakistan and India over the disputed Kashmir valley, where in 1947-1948 Pakistani army officers “used the Islamic notion of jihad to mobilize the tribesmen they had recruited as raiders for the seizure of Kashmir.” Thus, Haqqani concludes that despite the Pakistani army’s birth out of the British Indian army, “within the first few months of independence it was also moving in the direction of adopting an Islamic ideological coloring.”6

The military, however, did not have a smooth and seamless relationship with Pakistan’s Islamic parties. General Mohammad Ayub Khan, Pa-kistan’s first military ruler, displayed hostility toward the religious parties, writing in his diary in 1967 that “[t]he mullah regards the educated Muslims as his deadliest enemy and the rival for power,” and that “we have got to take on all those [mullahs] who are political mischief-makers.”7

Zulfikar Ali Bhutto, who became prime minister in 1973, broadened the ISI by creating an internal wing. He was concerned with bolstering his own political power, and his personal leadership had a paranoid strain. Thus, he wanted the ISI to conduct surveillance on friend and foe alike, and the agency kept dossiers on a range of figures. Ironically, the internal wing that Bhutto helped create would play a role in the military coup that toppled him from power in July 1977. The coup brought to power General Muhammad Zia ul-Haq, who would consciously push Pakistani society in a more religious direction, and would concentrate his efforts on the military in particular.

Stephen P. Cohen, a Pakistan expert at the Brookings Institution, points out that though Pakistan’s military shifted in an explicitly Islamic direction under Muhammad Zia ul-Haq, the army began Islamizing under Bhutto. “Zulfikar himself ordered alcohol removed from the mess,” Cohen says, “and one of the reasons that he picked Zia as the army’s chief of staff may have been that Zia was seen as a pious general.”8 Bhutto was not motivated by personal conviction in doing so: he was secular in outlook, but the Islamists were ascendant politically. This gesture was designed to placate them.

After executing a coup against Bhutto, Zia served as prime minister for around ten years, the longest tenure of any Pakistani executive. Zia was involved from an early age with the Tablighi Jamaat, a socially conservative grassroots religious movement. He had served in the Royal Indian Army prior to Pakistan’s creation, and his religiosity was apparent during his military service: he once explained that while other officers’ free time was occupied by drinking, gambling, and dancing, he spent his in prayer.9

Zia’s background and religious zeal translated into the adoption of overtly Muslim public policy positions, as well as the government’s imposition of Islamic norms and customs. These changes began immediately after the coup. One observer noted in early 1979 that a “general Islamic tone pervades everything.” He continued:

A state enterprise advertises for a manager “who should be a God fearing and practicing Muslim.” Floggings are common. Television has been greatly changed—to the accompaniment of public protest in the letters-to-the-editors column of the newspapers. Total closure of eating and drinking places between sunup and sunset marked Ramzan, the holy month of fasting, and no tea was served in business establishments or offices, private or public…. On December 2 [of 1978] (the first of Musharram, the beginning of the Hijri year 1399) came the long promised announcement of the first steps toward Islamization of the laws. Islamic laws on theft, drinking, adultery, and the protection of freedom of belief are to be enforced from [February 1979].10

Zia’s government created sharia courts to determine the religious legitimacy of all laws, and invalidate those that they deemed improper. The government simultaneously tried to create an “Islamic economy” that was free of interest.

Zia devoted particular attention to changing the culture of Pakistan’s military. His reforms went beyond Bhutto’s nascent changes in three major ways. First, the military’s training came to include Islamic teachings. For example, officers were required to read S. K. Malik’s The Quranic Concept of War, and a Directorate of Religious Instruction was created to oversee the Islamic education of the officer corps. Second, religious criteria were incorporated into the promotion requirements for officers, and into their promotion exams. Many skilled officers with secular outlooks were passed over for promotion, while many officers with conservative religious outlooks reached top levels of command. Third, Zia reinforced these policies by mandating formal obedience to Islamic rules within the military. He required not only that soldiers attend Friday congregational prayers at regimental mosques, but also that units bring mullahs with them to the front lines of combat.

At the same time that Zia was implementing these policies, the demographics of the officer corps were naturally shifting. The first generation of officers came from the country’s social elites, frequently educated in English-language schools, while the rank-and-file of the new junior officers came from Pakistan’s poorer northern districts. Journalist Zahid Hussain notes that “[t]he spirit of liberalism, common in the ‘old’ army, was practically unknown to them. They were products of a social class that, by its very nature, was conservative and easily influenced by Islamic fundamentalism.”11

Zia’s policies, coupled with the demographic shift in the junior officer corps, moved the military in a more religious, and more fundamentalist, direction. This new direction was also aided by external circumstances. Soon after Zia came to power, the Soviet Union invaded Afghanistan on behalf of a pro-Soviet regime that was threatened by Islamic rebels. This invasion would prove fateful. In addition to imposing great costs on the Soviet Union that would contribute to its collapse, the invasion spurred the U.S. and Pakistan to support anti-Soviet mujahideen. Thus, some of the changes to the organizational culture of Pakistan’s military pushed by Zia were put into practice on the battlefield. The ISI would grow exponentially during this period, and important relationships between Pakistani officials and Islamic militants would develop.

The Afghan crucible, and after

The Soviet Union invaded Afghanistan in 1979. Though the Soviets hoped to quickly secure the country for their proxy government, they became embroiled in a draining conflict.

The ISI was critical to anti-Soviet efforts. It funneled money to the mujahideen, and trained them. In doing so, the ISI benefited from significant foreign support, a large amount coming from the CIA. The CIA’s funding of the anti-Soviet resistance rose “from about $30 million in fiscal 1981 to about $200 million in fiscal 1984,”12 and reached about $500 million per year at its height. The money given to the ISI was effectively doubled by Saudi Arabia, which matched U.S. funding dollar for dollar during the Afghan-Soviet war.

The relationship between the CIA and ISI developed on the ISI’s terms, with Zia minimizing contact between the Americans and the Afghan mujahideen. This arrangement was mutually advantageous. It gave the Americans plausible deniability, gave the Pakistanis access to a large amount of American money, and allowed Pakistani officials to forge their own relationships with the mujahideen.

Though there were a range of mujahideen factions, the ISI preferred to fund extremist Islamic groups and ethnic separatists. There were two major reasons for this. One was strategic: the ISI perceived Islamists as fearless fighters, and believed they could more easily be transformed into a Pakistan proxy. A second reason was ideological: as Zia’s reforms promoting religion within Pakistan’s military took root, more officers came to sympathize with, or even adopt, a hard-line religious outlook.

As funding for the mujahideen grew, so did the ISI. Though it had a staff of around 2,000 prior to the Afghan-Soviet war, “the ISI grew to 20,000 employees during the height of the fight to remove the Soviets.”13 American funding for the war ended in 1989, when the Soviets withdrew from Afghanistan in defeat. Nonetheless, the ISI retained about 40,000 employees, and had a budget of around $1 billion “for maintaining influence among the now-victorious mujahideen groups.”14

After the Soviet Union retreated from Afghanistan, little united the disparate mujahideen factions other than their common fight against the Soviet-backed regime of Mohammad Najibullah. It is thus unsurprising that the country fell into civil war in 1992, after the mujahideen captured the capital of Kabul. Award-winning journalist Ahmed Rashid considers it significant that Kabul fell not to the Pashtun mujahideen factions, but rather to the better organized Tajik forces. “It was a devastating psychological blow because for the first time in 300 years the Pashtuns had lost control of the capital,” he writes in his definitive book about the Taliban. “An internal civil war began almost immediately.”15 Various warlords and former mujahideen vied for power in the capital and other strategic areas. The ISI remained involved during this period, and eventually became a major sponsor of the Taliban.

During the Afghan-Soviet war, a network of madrasas funded by Saudi Arabia sprang up near Pakistan’s border with Afghanistan. These schools served a strategic purpose: students were indoctrinated with a militant religious ideology designed to make them more fervent in the fight against the Soviets. This network of schools would ultimately give birth to the Taliban.

The Taliban emerged from Afghanistan’s chaos in 1994. There are a number of accounts of how the group formed, but Rashid finds one story to be the most credible. In this telling, two neighbors approached Mullah Mohammed Omar to inform him that a warlord “had abducted two teenage girls, their heads had been shaved and they had been taken to a military camp and repeatedly raped.” In response, Omar and thirty talibs “attacked the base, freeing the girls and hanging the commander from the barrel of a tank.”16

The Taliban’s power rapidly grew in Afghanistan because they were effective fighters, and they promised an alternative, albeit a ruthless one, to the prevailing lawlessness. Within two years of the group’s founding, it captured both Kandahar and Kabul. In doing so, the Taliban was aided by the ISI’s sponsorship. “The ISI helped the Taliban take the key cities of Jalalabad and the capital, Kabul,” the Christian Science Monitor reported, “and continued to back them as they secured about 95 percent of Afghanistan.”17 U.S. News and World Report further explained the close working relationship between the ISI and the Taliban: “ISI operatives permeated the regime, helping uneducated Taliban leaders with everything from fighting the opposition Northern Alliance to more mundane tasks like translating international documents.”18

As the Taliban expanded, it brought a harsh version of Islamic law. In his seminal 2001 book Holy War, Inc., journalist Peter Bergen referred to the Taliban’s voluminous restrictions as “Tali-bans.” He noted:

Soccer, kite-flying, music, television, and the presence of females in schools and offices were all banned. Some of the decrees had a Monty Python-esque quality, like the rule banning the use of paper bags on the remote chance the paper might include recycled pages of the Koran. Behavior the Taliban deemed deviant was met with inventive punishments. Taliban religious scholars labored over the vital question of how to deal with homosexuals: “Some say we should take these sinners to a high roof and throw them down, while others say we should dig a big hole beside a wall, bury them, then push the wall on top of them.”19

The Taliban offered Osama bin Laden and his followers safe haven in Afghanistan after they were forced to flee Sudan. Al-Qaeda established a network of training camps in Afghanistan; the 9/11 attacks were just one product of these camps. Significantly, while al-Qaeda found safe haven in Afghanistan, ISI agents formed relationships with the terrorist group. The New York Times has reported on the concerns of American officials that the ISI “even used Al Qaeda camps in Afghanistan to train covert operatives for use in a war of terror against India.”20 The Times noted that the ISI’s use of al-Qaeda camps to train fighters destined for Kashmir may have been revealed in August 1998, when the U.S. struck camps near Khost, Afghanistan, in retaliation for the bombing of U.S. embassies in Kenya and Tanzania. “The casualties included several members of a Kashmiri militant group supported by Pakistan who were believed to be training in the Qaeda camps,” the Times reported.21

The ISI supported the Taliban largely because the government in Kabul had historically been hostile to Pakistan, and Pakistan wanted its northern neighbor to be an ally. The Taliban’s fundamentalist religious ideology was a primary factor that convinced Pakistani planners that it could serve as their proxy, thus providing Pakistan with “strategic depth.” But the ideological reasons behind the ISI’s support for the Taliban were also growing: militant Islamic ideology within Pakistan’s military and ISI has increased over time.

Resistant to reform

Shortly after 9/11, U.S. deputy secretary of state Richard Armitage gave Pakistan the ultimatum that, in Musharraf’s words, “we had to decide whether we were with America or with the terrorists, but that if we chose the terrorists, then we should be prepared to be bombed back to the Stone Age.”22 The first major battlefield in the war on terror was Afghanistan, and Pakistan’s geographic proximity and historical support for the Taliban made it strategically important. Armitage’s threat (along with several carrots) prompted Musharraf to announce a dramatic about-face, and closely align with the U.S. Mu-sharraf declared on January 12, 2002, that “no Pakistan-based organization would be allowed to indulge in terrorism in the name of religion.”23 He banned five jihadist groups that day, including Lashkar-e-Taiba and Jaish-e-Mohammed.

The ISI had already developed a distinctive strategic and ideological outlook prior to 9/11 that favored support for stateless Islamist fighters. Hence, along with his changed policies, Musharraf sacked pro-Taliban commanders at the top levels of the ISI and military. Altogether, he “forced the reassignment or resignation of Pakistan’s intelligence chief, two top generals and a number of other military commanders—most of whom were regarded as pro-Taliban or Islamist.”24

In addition to the firings, Mu-sharraf made other changes aimed at purging officers with extremist sympathies from the military and ISI. In February 2002, for example, Pakistan began “to disband two major units of its powerful intelligence service that had close links to Islamic militants in Afghanistan and Kashmir.”25 But this was not enough to transform the strategic and ideological outlook of either institution. Many military and ISI officers remained tied to the Taliban militants and mujahideen with whom they had built relations over the course of two decades. Moreover, the Frankenstein monster of Pakistan-created jihadist groups was now out of control: Pakistan created many such groups, and supported them for over a decade. It couldn’t simply cut them all off at once.

Today, support for jihadist groups occurs at three levels within Pakistan’s ISI and military. First, there is an institutional policy of support within the ISI for actors such as the Haqqani network, Mullah Omar’s Taliban, and perhaps other jihadist groups that have ties to al-Qaeda at top levels.

Second, beyond the ISI’s explicit policies, rogue elements of Pakistan’s ISI and military have provided support for jihadist groups against the policies of their institutions. These elements have been implicated in several recent terrorist incidents, and peripheral evidence suggests that these may only be the tip of the iceberg. Major incidents where rogue elements within Pakistan’s ISI or military may have been involved include the November 2008 Mumbai attacks, the July 2008 bombing of India’s embassy in Kabul, the September 2008 Islamabad Marriott bombing, and assassination attempts directed at Pervez Musharraf and Benazir Bhutto. However, few—if any—Western analysts have a good sense of what percentage of people within the ISI support jihadist groups against the policies of Pakistan’s government. There is also an open question as to whether these rogue elements are acting individually, or if they constitute factions within the ISI and the military.

Third, retired ISI and military officers with connections to Islamic militancy often remain influential following their retirement. One example is former ISI head Hamid Gul, who in 2003 declared that “God will destroy the United States in Iraq and Afghanistan and wherever it will try to go from there.” In late 2008, the U.S. sent a secret document to Pakistan’s government linking Gul to the Taliban and al-Qaeda, and India has demanded his arrest in connection with the November 2008 Mumbai terrorist attacks.26

There is frequently overlap between these three levels. For example, retired ISI officers frequently work for the organization as contractors, and a number of analysts believe that contractors are the strongest link insofar as support for jihadist groups against the ISI’s policies is concerned. It is clear that all three levels of support create problems for U.S. interests in the region, while strengthening jihadist groups.


Few options for addressing support for religious militancy in Pakistan’s military and ISI are easy or certain to work. Because of the importance of the problem, and the uncertainty of the solutions, the U.S. should be willing to try several options simultaneously. Though not all of them will bear fruit, tackling the problem in multiple ways will allow the U.S. to build on its successes.

The overarching goal of U.S. diplomacy with Pakistan should be to persuade Pakistan’s government to cease support for jihadist groups where there is an institutional policy of doing so, and to conduct operations on its own soil against these groups. Any U.S. policy in this regard should include both carrots and sticks. The diplomacy should not be loud and blustering; it needs to be direct yet behind the scenes. One reason that Musharraf’s party was trounced in the February 2008 parliamentary elections is that he was popularly seen as an American puppet. Diplomatic pressure that is too overt may put Pakistani politicians in a position where they jeopardize their political future by doing the right thing.

One interesting diplomatic route for the U.S. is entering into a dialogue with Pakistan about how to ameliorate its security concerns. Pakistani planners have always cited strategic depth as a reason that they support stateless Islamic militants, particularly in Afghanistan and Kashmir. The U.S. has not engaged in dialogue with Pakistan about its security concerns before.

Some sticks that the U.S. can use in its diplomacy with Pakistan are obvious, such as the threat of lessening economic assistance. Seth Jones, a Pakistan expert with the RAND Corporation, says that U.S. assistance should be tied to the arrest or killing of key al-Qaeda leaders such as Ayman al-Zawahiri. “The threat then would be that if we can’t get clear progress in a measurable timeframe, this would leave the United States in the unfortunate position of having to significantly decrease its assistance to Pakistan and move in the direction of India.” Jones thinks this pressure should be aimed at getting Pakistan’s military and intelligence services to undertake a “clear and hold strategy” against al-Qaeda safe havens—not as a military offensive, but as a police and intelligence operation.27

One interesting fact is that conducting military operations on Pakistani soil can function as a stick, given the frequently apoplectic reaction to such operations by Pakistani leadership. The threat of such operations can have a coercive effect.

The U.S. can also take steps, albeit relatively modest ones, to bolster actors within Pakistan’s military and ISI that are opposed to religious militancy. For example, the U.S. could enhance the prestige of commanders and units within Pakistan’s military who willingly cooperate in counterinsurgency operations by earmarking military aid for specific regiments or commanders. Similarly, high-level U.S. military training could focus on units and commanders who have demonstrated their willingness to undertake military or policing efforts against extremist groups.

Zahid Hussain observed that when Musharraf allied with the United States after 9/11, the president was “taking Pakistan to war with itself.”28 While a complex set of policies, conflicts, and geopolitical circumstances pushed Pakistan’s military and ISI toward support of stateless religious militants, later efforts to reverse these policies have not been as vigorous. And for that, both Pakistan and the U.S. are now paying a price. Whatever road we take in Pakistan will involve a substantial time commitment, and progress is likely to be slow. But it is vital to develop a coherent Pakistan policy.

Daveed Gartenstein-Ross is the vice president of research at the Foundation for Defense of Democracies, where he directs the Center for Terrorism Research. He is currently a Ph.D. candidate in world politics at the Catholic University of America.

  1. Mark Mazzetti & Eric Schmitt, “C.I.A. Outlines Pakistan Links with Militants,” New York Times, July 30, 2008.
  2. The formulation “war on terror” has always been both inadequate and inaccurate, and there are signs that Barack Obama’s administration may abandon this phraseology. See Michael Isikoff & Mark Hosenball, “War on Words: Why Obama May Be Abandoning Bush’s Favorite Phrase,” Newsweek, Feb. 4, 2009.
  3. Zahid Hussain, Frontline Pakistan: The Struggle with Militant Islam (New York: Columbia University Press, 2007), 13.
  4. Shuja Nawaz, Crossed Swords: Pakistan, Its Army, and the Wars Within (Oxford: Oxford University Press, 2008), xxxi.
  5. Husain Haqqani, Pakistan: Between Mosque and Military (Washington, DC: Carnegie Endowment for International Peace, 2005), 2-3.
  6. Ibid., 29.
  7. As reprinted in Craig Baxter, ed., Diaries of Field Marshal Mohammad Ayub Khan 1966-1972 (Karachi: Oxford University Press, 2007), 49.
  8. Author’s telephone interview, November 24, 2008.
  9. Haqqani, Pakistan: Between Mosque and Military, 132.
  10. W. Eric Gustafson, “Pakistan 1978: At the Brink Again?” Asian Survey, February 1979, 161-62.
  11. Hussain, Frontline Pakistan, 20.
  12. Steve Coll, Ghost Wars: The Secret History of the CIA, Afghanistan, and Bin Laden, from the Soviet Invasion to September 10, 2001 (New York: Penguin Books, 2004), 65.
  13. Robert Marquand & Scott Baldauf, “Will Spies Who Know Tell the U.S.?” Christian Science Monitor, October 3, 2001.
  14. Ibid.
  15. Ahmed Rashid, Taliban: Militant Islam, Oil and Fundamentalism in Central Asia (New Haven: Yale University Press, 2000), 21.
  16. Ibid., 25.
  17. Marquand & Baldauf, “Will Spies Who Know Tell the U.S.?”
  18. Michael Schaffer, “The Unseen Power,” U.S. News & World Report, November 4, 2001.
  19. Peter Bergen, Holy War, Inc.: Inside the Secret World of Osama bin Laden (New York: The Free Press, 2001), 9.
  20. James Risen & Judith Miller, “Pakistani Intelligence Had Links to Al Qaeda, U.S. Officials Say,” New York Times, October 29, 2001.
  21. Ibid.
  22. Pervez Musharraf, In the Line of Fire: A Memoir (New York: Free Press, 2006), 201.
  23. Hussain, Frontline Pakistan, 51.
  24. Refet Kaplan, “Pakistani President Purges Pro-Taliban Military Leaders,”, October 8, 2001.
  25. Douglas Jehl, “Pakistan to Cut Islamists’ Links to Spy Agency,” New York Times, February 20, 2002.
  26. See Ansar Abbasi, “Secret Document Confirms Hameed Gul Wanted by the U.S.,” International News (Pakistan), December 7, 2008 (describing secret U.S. document); Emily Wax & Rama Lakshmi, “Indian Official Points to Pakistan,” Washington Post, December 6, 2008 (describing the Indian demand for Gul’s arrest).
  27. Quoted in Daveed Gartenstein-Ross, “While Pakistan Burns,” Weekly Standard, October 29, 2007.
  28. Hussain, Frontline Pakistan, p. viii.

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