NATO's commander in Afghanistan, U.S. General David McKiernan, said this week he is certain there is "a level of ISI complicity" in the militant areas of Pakistan and within organizations like the Taliban.
McKiernan's remarks echo allegations made by Afghan President Hamid Karzai, the Indian government, and Pentagon insiders who are frustrated about the rising cross-border militancy that is based in Pakistan.
But McKiernan said he is unable to speak about the level of leadership within Pakistan's Inter-Services Intelligence (ISI) agency that is involved with the Taliban and other militants.
Pakistan has refuted allegations that the ISI supports cross-border insurgent attacks into Afghanistan. Islamabad does acknowledge that elements within the ISI are sympathetic to the insurgency in Afghanistan. But it portrays such agents as "rogue" operators pursuing their own private agendas.
Barnett Rubin, director of New York University's Center on International Cooperation, tells RFE/RL that he thinks the ISI is too disciplined for rogue agents to carry out such activities without getting caught.
"Whatever is happening, I don't think it is attributable to rogue elements," Rubin says. "In any intelligence service -- especially for covert operations -- you often try to maintain a level of deniability so that the top decision makers are not fully informed about what is going on."
Level Of Deniability
Pakistani journalist Ahmed Rashid, author of the book "Taliban," has maintained for years that the ISI has played a double game with Washington and the Taliban.
On the one hand, Pakistan is a key U.S. ally in the war against terrorism. At the same time, the ISI is alleged to covertly support cross-border militant attacks in neighboring Afghanistan, India, and the Indian-administered parts of Kashmir.
In his latest book, "Descent Into Chaos," Rashid maintains that the ISI has set up private organizations in order to distance the relationship between its military leadership and extremist fighters. He says the private organizations are staffed by retired ISI officers and funded through the budget of Pakistan's Frontier Corps.
The scenario described by Rashid highlights the lack of oversight that the civilian government in Islamabad has over the ISI.
"There are still huge differences between the military and the politicians as to how to combat terrorism -- what to do about it. The military is really controlling the policy. The civilians don't have much of a say," Rashid says.
"This is one of the reasons why Pakistan has not been able to fight the war on terror decisively and why there are so many differences with the Americans on this. Not everyone is reading from the same page."
Rubin says that although the ISI is nominally controlled by the Pakistani prime minister, the reality is that it is controlled by Pakistan's armed forces.
"Formally, the [director-general] of the ISI reports to the prime minister. The [director-general] of the ISI, however, is a three-star general appointed by the chief of army staff, who reports to the president. The eight departments of the ISI are headed by eight two-star generals who are chosen by the [director-general of the] ISI. And the budget comes out of the defense and intelligence budget, which is not subject to civilian review in Pakistan," Rubin says.
"So, while formally [the ISI] reports to the prime minister, the control is effectively lodged with the military," he adds. "Now how that actually works -- that is, who finally makes decisions -- I don't know."
Nasim Zehra, a prominent Pakistani journalist and security analyst, as well as a research fellow for Harvard University's Asia Center, points out that the "ISI is heavily manned by people from the armed forces. So it is not an organization which is a purely civilian organization.
"It would be correct to say that it has not been controlled, really, by the prime minister the way it should be. Technically and constitutionally, it is under the control of the prime minister. But operationally speaking, and substantively speaking, the prime ministers have not really even strengthened the defense cabinet committees," Zehra adds. "As the ISI stands today, it pretty much doesn't function under these kind of parliament-related civilian controls."
Continuing The Jihad
Indeed, the top military generals in charge of Pakistan's army and the ISI were appointed by President Pervez Musharraf after he seized power in 1999 in a bloodless coup.
Musharraf -- who also held the country's top military post until he resigned late last year as chief of the army staff -- now faces the prospect of impeachment by the governing coalition in Pakistan. Musharraf is accused of misconduct and violating the constitution.
Rashid says Pakistan's army never understood that after the September 11, 2001, terrorist attacks in the United States, the international community would have no tolerance for Islamic extremism and that the ISI's backing of militant groups would have to cease, not just in Afghanistan, but also in Kashmir.
Zehra says the ISI grew by leaps and bounds when an "international jihad" against the Soviet invasion of Afghanistan was being bankrolled through Pakistan with funds from the United States, Britain, Saudi Arabia, and other countries. She says that is when the ISI grew in capacity, skill, and resources as an agency capable of carrying out covert operations externally.
"Past that period, the ISI strategy that has flowered -- the training that was given -- was really essentially...'religionized militancy' and 'Islamicized militancy,'" Zehra says.
"And the tools -- the assets -- that were developed by the intelligence agency were subsequently used to reach [the goals of] Pakistan's own security interests and [for] battling Pakistan's own security threats as perceived by intelligence agencies in Pakistan."
Question Of Politics
But Zehra says it is the ISI's political machinations within Pakistan, rather than its external activities, that have damaged its reputation among Pakistanis.
"This country has been under military rule quite a lot. When it has been under military rule, one section of the ISI has been used by military rulers to engineer the political situation in the country," Zehra says. "And for that it has earned a very bad reputation."
As a result, Zehra says the issue of civilian oversight for the ISI is now very important to Pakistan's governing coalition.
"Internally, obviously, there has always been a big question that we need to have an organization which reports to the executive -- and the reporting lines are stringent and there is oversight. That's the concern within the country," Zehra says.
"There has been an effort in the past under General Musharraf -- the question of growing a nexus between the executive authority and the ISI so that there is unity of command. General Musharraf has been very keen that the intelligence agency would come completely under his control," Zehra adds. "Now the question, of course, is: With an elected government, how do you arrange this control of the ISI?"
Zehra concludes that regardless of what happens with the coalition's efforts to impeach Musharraf, officials in Islamabad need to ensure rigorous lines of authority for the ISI in the future.
She says one possible avenue is having the defense cabinet committee -- as well as parliamentary committees -- oversee the ISI. But Zehra adds that the path of institutional accession -- the supremacy of the parliament as laid out in the constitution -- means that the parliament also needs to get serious on this issue. An issue that is not only important to Pakistanis -- but also very important to Pakistan's neighbors and the country's allies in the war against terrorism.