A top Central Intelligence Agency official traveled secretly to Islamabad this month to confront Pakistan‘s most senior officials with new information about ties between the country’s powerful spy service and militants operating in Pakistan’s tribal areas, according to American military and intelligence officials.
The C.I.A. emissary presented evidence showing that members of the spy service had deepened their ties with some militant groups that were responsible for a surge of violence in Afghanistan, possibly including the suicide bombing this month of the Indian Embassy in Kabul, the officials said.
The decision to confront Pakistan with what the officials described as a new C.I.A. assessment of the spy service’s activities seemed to be the bluntest American warning to Pakistan since shortly after the Sept. 11 attacks about the ties between the spy service and Islamic militants.
The C.I.A. assessment specifically points to links between members of the spy service, the Directorate for Inter-Services Intelligence, or ISI, and the militant network led by Maulavi Jalaluddin Haqqani, which American officials believe maintains close ties to senior figures of Al Qaeda in Pakistan’s tribal areas.
The C.I.A. has depended heavily on the ISI for information about militants in Pakistan, despite longstanding concerns about divided loyalties within the Pakistani spy service, which had close relations with the Taliban in Afghanistan before the Sept. 11 attacks.
That ISI officers have maintained important ties to anti-American militants has been the subject of previous reports in The New York Times. But the C.I.A. and the Bush administration have generally sought to avoid criticism of Pakistan, which they regard as a crucial ally in the fight against terrorism.
The visit to Pakistan by the C.I.A. official, Stephen R. Kappes, the agency’s deputy director, was described by several American military and intelligence officials in interviews in recent days. Some of those who were interviewed made clear that they welcomed the decision by the C.I.A. to take a harder line toward the ISI’s dealings with militant groups.
Pakistan’s prime minister, Yousaf Raza Gilani, is currently in Washington meeting with Bush administration officials. A White House spokesman, Gordon D. Johndroe, would not say whether President Bush had raised the issue during his meeting on Monday with Mr. Gilani. In an interview broadcast Tuesday on the PBS program “The NewsHour with Jim Lehrer,” Mr. Gilani said he rejected as “not believable” any assertions of ISI’s links to the militants. “We would not allow that,” he said.
The Haqqani network and other militants operating in the tribal areas along the Afghan border are said by American intelligence officials to be responsible for increasingly deadly and complex attacks inside Afghanistan, and to have helped Al Qaeda establish a safe haven in the tribal areas.
Lt. Gen. Martin E. Dempsey, the acting commander of American forces in Southwest Asia, made an unannounced visit to the tribal areas on Monday, a further reflection of American concern.
The ISI has for decades maintained contacts with various militant groups in the tribal areas and elsewhere, both for gathering intelligence and as proxies to exert influence on neighboring India and Afghanistan. It is unclear whether the C.I.A. officials have concluded that contacts between the ISI and militant groups are blessed at the highest levels of Pakistan’s spy service and military, or are carried out by rogue elements of Pakistan’s security apparatus.
With Pakistan’s new civilian government struggling to assert control over the country’s spy service, there are concerns in Washington that the ISI may become even more powerful than when President Pervez Musharraf controlled the military and the government. Last weekend, Pakistani military and intelligence officials thwarted an attempt by the government in Islamabad to put the ISI more directly under civilian control.
“It was a very pointed message saying, ‘Look, we know there’s a connection, not just with Haqqani but also with other bad guys and ISI, and we think you could do more and we want you to do more about it,’ ” one senior American official said of the message to Pakistan. The official was briefed on the meetings; like others who agreed to talk about it, he spoke on condition of anonymity because of the diplomatic delicacy of Mr. Kappes’s message.
The meetings took place days after a suicide bomber attacked the Indian Embassy in Kabul, killing dozens. Afghanistan’s government has publicly accused the ISI of having a hand in the attack, an assertion American officials have not corroborated.
The decision to have Mr. Kappes deliver the message about the spy service was an unusual one, and could be a sign that the relationship between the C.I.A. and the ISI, which has long been marked by mutual suspicion as well as mutual dependence, may be deteriorating.
The trip is reminiscent of a secret visit that the top two American intelligence officials made to Pakistan in January. Those officials – Mike McConnell, the director of national intelligence, and Michael V. Hayden, the C.I.A. director – sought to press Mr. Musharraf to allow the C.I.A. greater latitude to operate in the tribal territories.
It was the ISI, backed by millions of covert dollars from the C.I.A., that ran arms to guerrillas fighting Soviet forces in Afghanistan in the 1980s. It is now American troops who are dying in Afghanistan, and intelligence officials believe those longstanding ties between Pakistani spies and militants may be part of an effort to destabilize Afghanistan.
Spokesmen for the White House and the C.I.A. declined to comment about the visit by Mr. Kappes or about the agency’s assessment. A spokesman for Admiral Mullen, Capt. John Kirby, declined to comment on the meetings, saying “the chairman desires to keep these meetings private and therefore it would be inappropriate to discuss any details.”
Admiral Mullen and Mr. Kappes met in Islamabad with several high-ranking Pakistani officials. They included Mr. Gilani; Mr. Musharraf; Gen. Ashfaq Parvez Kayani, the army chief of staff and former ISI director; and Lt. Gen. Nadeem Taj, the current ISI director.
One American counterterrorism official said there was no evidence of Pakistan’s government’s direct support of Al Qaeda. He said, however, there were “genuine and longstanding concerns about Pakistan’s ties to the Haqqani network, which of course has links to Al Qaeda.”
American commanders in Afghanistan have in recent months sounded an increasingly shrill alarm about the threat posed by Mr. Haqqani’s network. Earlier this year, American military officials pressed the American ambassador in Pakistan, Anne W. Patterson, to get Pakistani troops to strike Haqqani network targets in the tribal areas.
Gen. Dan K. McNeill, the senior NATO commander in Afghanistan until last month, frequently discussed the ISI’s contacts with militant groups with General Kayani, Pakistan’s military chief.
During his visit to the tribal areas on Monday, General Dempsey met with top Pakistani commanders in Miramshah, the capital of North Waziristan, where Pakistan’s 11th Army Corps and Frontier Corps paramilitary force have a headquarters, to discuss the security situation in the region, Pakistani officials said.
North Waziristan, the most lawless of the tribal areas, is a hub of Al Qaeda and other foreign fighters, and the base of operations for the Haqqani network.
On Tuesday, Pakistani security forces raided an abandoned seminary owned by Mr. Haqqani, Pakistani officials said. No arrests were made.
Ismail Khan contributed reporting from Peshawar, Pakistan.
Date: July 30, 2008