most C.I.A. veterans agree that no relationship between the spy agency and a foreign intelligence service is quite as byzantine, or as maddening, as that between the C.I.A. and Pakistan’s Directorate for Inter-Services Intelligence, or I.S.I.

It is like a bad marriage in which both spouses have long stopped trusting each other, but would never think of breaking up because they have become so mutually dependent.

Without the I.S.I.’s help, American spies in Pakistan would be incapable of carrying out their primary mission in the country: hunting Islamic militants, including top members of Al Qaeda. Without the millions of covert American dollars sent annually to Pakistan, the I.S.I. would have trouble competing with the spy service of its archrival, India.

There have been bitter fights between the C.I.A. station chiefs in Kabul and Islamabad, particularly about the significance of the militant threat in the tribal areas. At times, the view from Kabul has been not only that the I.S.I. is actively aiding the militants, but that C.I.A. officers in Pakistan refuse to confront the I.S.I. over the issue.

Veterans of the C.I.A. station in Islamabad point to the capture of a number of senior Qaeda leaders in Pakistan in recent years as proof that the Pakistani intelligence service has often shown a serious commitment to roll up terror networks. It was the I.S.I., they say, that did much of the legwork leading to the capture of operatives like Khalid Sheikh Mohammed, Abu Zubaydah and Ramzi bin al-Shibh.

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.

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.

The grumbling at the C.I.A. about dealing with Pakistan’s I.S.I. comes with a certain grudging reverence for the spy service’s Machiavellian qualities. Some former spies even talk about the Pakistani agency with a mix of awe and professional jealousy.

One senior C.I.A. official, recently retired, said that of all the foreign spymasters the C.I.A. had dealt with, General Kayani was the most formidable and may have earned the most respect at C.I.A. headquarters in Langley, Va. The soft-spoken general, he said, is a master manipulator.

“We admire those traits,” he said.