A top official of CIA has secretly travelled to Islamabad this month and confronted Pakistan's senior officials with new information about deepening ties between the ISI and the militants operating in tribal areas, the New York Times said quoting American military and intelligence officials.

CIA's deputy director, Stephen R Kappes, secret visit to Pakistan on July 12, along with Adm Mike Mullen, chairman of the Joint Chief of Staff, was described by several American military and intelligence officials in interviews to the daily, who made it clear that they welcomed the decision by the CIA to take a harder line toward the ISI's dealings with militant groups.

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 paper said.

The decision to have Kappes deliver the message about the spy service could be a sign of deteriorating relationship between the CIA and the ISI, which has long been marked by mutual suspicion and dependence, the report said.

The CIA 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 Taliban in Afghanistan before the September 11 attacks.

The CIA assessment specifically points to links between the members of the ISI, and the militant network led by Maulavi Jalauddin Haqqani which according to America has close ties with senior figures of al-Qaeda in Pakistan's tribal areas.

Pakistan's Prime Minister Yousaf Raza Gilani, who is currently in Washington to hold meeting with US administration officials, had in an interview broadcasted on Tuesday on a local news channel, rejected as "not believable" any assertions of ISI's links to the militants.

"We would not allow that," he was quoted as saying by the daily. Lt Gen Martin E Dempsey, the acting commander of American forces in Southwest Asia, had also made an unannounced visit to the tribal areas on Monday, further reflecting US concern towards growing ties between Pak officials and militants.

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 neighbouring India and Afghanistan.

It was the ISI, backed by millions of covert dollars from the CIA, that ran arms to guerrillas fighting Soviet forces in Afghanistan in the 1980s. It is now American troops who are dying in Afghanistan, and the intelligence officials believe those longstanding ties between Pakistani spies and militants may be part of an effort to destabilise Afghanistan.