The ISI and Terrorism: Behind the Accusations

Eben Kaplan, Associate Editor; Jayshree Bajoria, Staff Writer
Council on Foreign Relations
Wednesday, July 9, 2008; 10:12 AM


Pakistan's intelligence agency, the Inter-Services Intelligence (ISI), has long faced accusations of meddling in the affairs of its neighbors. A range of officials inside and outside Pakistan have stepped up suggestions of links between the ISI and terrorist groups in recent years. In autumn 2006, a leaked report by a British Defense Ministry think tank charged, "Indirectly Pakistan (through the ISI) has been supporting terrorism and extremism -- whether in London on 7/7, or in Afghanistan, or Iraq." In June 2008, Afghan officials accused Pakistan's intelligence service of plotting a failed assassination attempt on President Hamid Karzai; shortly thereafter, they implied the ISI's involvement in a July 2008 attack on the Indian embassy. In an October 2006 interview, Pakistani President Pervez Musharraf said some retired ISI operatives could be abetting the Taliban insurgency in Afghanistan, but he denied any active links. Pakistan's government has repeatedly denied allegations of supporting terrorism, citing as evidence its cooperation in the "war on terror," in which it has taken significant losses both politically and on the battlefield.

Supporting Terrorism?

"The ISI probably would not define what they've done in the past as 'terrorism,'" says William Milam, former U.S. ambassador to Pakistan. Nevertheless, experts say the ISI has supported a number of militant groups in the disputed Kashmir region between Pakistan and India, some of which are on the State Department's Foreign Terrorist Organizations list. While Pakistan has a formidable military presence near the Indian border, some experts believe the relationship between the military and some Kashmiri groups has greatly changed with the rise of militancy within Pakistan. Shuja Nawaz,author of the book Crossed Swords: Pakistan, its Army, and the Wars Within, says the ISI "has certainly lost control" of Kashmiri militant groups. According to Nawaz, some of the groups trained by the ISI to fuel insurgency in Kashmir have been implicated in bombings and attacks within Pakistan, therefore making them army targets.

On Pakistan's western border with Afghanistan, the ISI supported the Taliban up to September 11, 2001, though Pakistani officials deny any current support for the group. The ISI's first major involvement in Afghanistan came after the Soviet invasion in 1979, when it partnered with the CIA to provide weapons, money, intelligence, and training to the mujahadeen fighting the Red Army. At the time, some voices within the United States questioned the degree to which Pakistani intelligence favored extremist and anti-American fighters. Following the Soviet withdrawal, the ISI continued its involvement in Afghanistan, first supporting resistance fighters opposed to Moscow's puppet government, and later the Taliban.

Pakistan stands accused of allowing that support to continue. Afghan President Hamid Karzai has repeatedly said Pakistan trains militants and sends them across the border. In May 2006, the British chief of staff for southern Afghanistan told the Guardian, "The thinking piece of the Taliban is out of Quetta in Pakistan. It's the major headquarters." Speaking at the Council on Foreign Relations in September 2006, President Musharraf responded to such accusations, saying, "It is the most ridiculous thought that the Taliban headquarters can be in Quetta." Nevertheless, experts generally suspect Pakistan still provides some support to the Taliban, though probably not to the extent it did in the past. "If they're giving them support," Kathy Gannon, who covered the region for decades for the Associated Press says, "it's access back and forth [to Afghanistan] and the ability to find safe haven."

Many in the Pakistani government, including slain former Prime Minister Benazir Bhutto, have called the intelligence agency "a state within a state," working beyond the government's control and pursuing its own foreign policy. But Nawaz says the intelligence agency does not function independently. "It aligns itself to the power center," and does what the government or the army asks it to do, says Nawaz.

Control over the ISI

Constitutionally, the agency is acountable to the prime minister, says Hassan Abbas, research fellow at Harvard's Kennedy School of Government. But most officers in the ISI are from the army, so that is where their loyalties and interests lie, he says. Experts say until the end of 2007, as army chief and president, Musharraf exercised firm control over the intelligence agency. But now, Abbas says, "he is the third player in the game." With a new army chief and a new prime minister in Pakistan gaining increasing control of the agency, Musharraf has no direct control over it. But he still wields influence, Abbas says, in the form of a close former associate, Lieutenant-General Nadeem Taj, who heads the intelligence agency.

"I do not accept the thesis that the ISI is a rogue organization," Milam says. "It's a disciplined army unit that does what it's told, though it may push the envelope sometimes." With a reported staff of ten thousand, ISI is hardly monolithic: "Like in any secret service, there are rogue elements," says Frederic Grare, a South Asia expert and visiting scholar at the Carnegie Endowment for International Peace. He points out that many of the ISI's agents have ethnic and cultural ties to Afghan insurgents, and naturally sympathize with them. Marvin G. Weinbaum, an expert on Afghanistan and Pakistan at the Middle East Institute, says Pakistan has sent "retired" ISI agents on missions the government could not officially endorse. Some observers believe Pakistan's duplicity is deliberate: "Musharraf's been playing with us since day one," Grare says.

Resistance in FATA

Pakistan's tribal areas along the Afghan border have emerged as safe havens for terrorists. Experts say because of their links to the Taliban and other militant groups, the ISI has some influence in the region. But with the mushrooming of armed groups in the tribal agencies, it is hard to say which ones the agency controls. Also, there appears to be division within the ISI. While some within the intelligence agency continue to sympathize with the militant groups, Harvard's Abbas says others realise they cannot follow a policy contradictory to that of the army, which is directly involved in counterterrorism operations in the area.

Mixed Record on Counterterrorism

Pakistan has arrested scores of al-Qaeda affiliates, including Khalid Sheikh
Mohammed, the alleged mastermind of the 9/11 attacks. The ISI and the Pakistani military have worked effectively with the United States to pursue the remnants of al-Qaeda. Following 9/11, Pakistan also stationed eighty thousand troops in the troubled province of Waziristan near the Afghan border. Hundreds of Pakistani soldiers died there in resulting clashes with militants, which in 2006 Musharraf told a CFR meeting "broke the al-Qaeda network's back in Pakistan."

But Musharraf has cracked down on terrorist groups selectively, as this Backgrounder points out. Weinbaum in 2006 said the Pakistani military has largely ignored Taliban fighters on its soil. "There are extremist groups that are beyond the pale with which the ISI has no influence at all," he says. "Those are the ones they go after." In spring 2008, Ashley J. Tellis, senior associate at the Carnegie Endowment for International Peace, writes (PDF) in The Washington Quarterly that Musharraf tightened pressure on groups whose objectives were out of sync with the military's perception of Pakistan's national interest.

Taliban as a Strategic Asset

Pakistan does not enjoy good relations with the current leadership of Afghanistan, partly because of rhetorical clashes with Afghan President Hamid Karzai, and partly because Karzai has made strong ties to India. Some experts say Pakistan wants to see a stable, friendlier government emerge in Afghanistan. Though the insurgency certainly doesn't serve this goal, increased Taliban influence, especially in the government, might. Supporting the Taliban also allows Pakistan to hedge its bets should the NATO coalition pull out of Afghanistan. In a February 2008 interview with, Tellis said the Pakistani intelligence services continue to support the Taliban because they see the Taliban leadership "as a strategic asset," a reliable back-up force in case things go sour in Afghanistan.

Not everyone agrees with this analysis. According to Weinbaum, Pakistan has two policies. One is an official policy of promoting stability in Afghanistan; the other is an unofficial policy of supporting jihadis in order to appease political forces within Pakistan. "The second [policy] undermines the first one," he says. Nawaz says there is ambivalence within the army regarding support for the Taliban. "They'd rather not deal with the Afghan Taliban as an adversary," he says.

Allegations of Terrorist Attacks

Indian officials claim to have evidence that the ISI planned the July 2006 bombing of the Mumbai commuter trains, but the charges seem unlikely to some observers of the long, difficult India-Pakistan relationship. The two nations have a history of finger-pointing, and while some of the allegations hold water, there is a tendency to exaggerate. Furthermore, endorsing an attack on India would undermine Musharraf's own policy. "Pakistan is genuinely trying to open up relations with India," Gannon says.

In Weinbaum's view, the British report regarding its July 2005 bombings -- which London insists is not a statement of policy -- makes "too broad a statement." Though Pakistan does offer safe haven to Kashmiri groups, and perhaps some Taliban fighters, the suggestion that the ISI is responsible for the 7/7 bombings of London's mass transit system is "a real stretch," Gannon says.

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