NEW YORK - Prime Minister Yousuf Raza Gilani has rejected as "not believable" any assertions about ties between Pakistan's Inter-Services Intelligence and militants operating in the country's tribal areas. "We would not allow that," he said in response to a pointed question on an American television channel Tuesday evening, but on Wednesday The New York Times carried a front-page report, saying that the CIA, the US spy agency, earlier this month confronted senior Pakistani officials with evidence showing members of ISI have deepened their ties with some militant groups responsible for a surge of violence in Afghanistan, possibly including the suicide bombing this month of the Indian embassy in Kabul. "(W)e would never expect our ISI, which is a very competent, so that there is anybody who's a sympathizer, we will not allow that, because the ISI is directly working under the prime minister," Gilani said PBS programme "The NewsHour with Jim Lehrer." A White House spokesman, Gordon Johndroe, would not say whether President Bush had raised the issue during his meeting on Monday with Mr Gilani. Today's Times' report said a top CIA official travelled to Islamabad this month with new information about ties between ISI and militants operating in Pakistan's tribal areas. Its sources were stated to be American military and intelligence officials who were not identified. The Times said the CIA assessment pointed to links between the ISI and the militant network led by Jalaluddin Haqqani, which American officials believe maintains close ties to senior figures of al-Qaeda in Pakistan's tribal areas. The CIA has depended heavily on the ISI for information about militants in Pakistan despite long-standing concerns about divided loyalties within the Pakistani spy service, which had close relations with the Taliban in Afghanistan before the Sept 11, 2001 attacks. The visit to Pakistan by the CIA official, Stephen Kappes, the agency's deputy director, was described by several American military and intelligence officials in interviews in recent days, the Times said. Some of those who were interviewed, it said, made clear that they welcomed the decision by the CIA to take a harder line towards the ISI's dealings with militant groups. "It was a very pointed message saying, 'Look, we know there's a connection, not just with Haqqani but also with the other bad guys and ISI, and we think you could do more and we want you to do more about it," a senior US officials told the Times, referring to ISI. The daily said the meeting could be a sign that the relationship between the Central Intelligence Agency and Pakistan's ISI "may be deteriorating". A US official said there was no evidence of official Pakistani support of Al-Qaeda, but there was "genuine and longstanding concerns about Pakistan's ties to the Haqqani network, which of course has ties to Al-Qaeda." The report comes after premier Gilani met with US President George W Bush in Washington and urged him not to act "unilaterally" against militants in Pakistan's lawless tribal zones. The newspaper said it was unclear whether CIA 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. Kappes made his secret visit to Pakistan on July 12, joining Admiral Mike Mullen, the chairman of the Joint Chiefs of Staff, for meetings with senior Pakistani civilian and military leaders, the Times said. 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. The Times' dispatch said, "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." AFP adds:  Military Wednesday rejected a "malicious" report that a top CIA official visiting this month confronted Islamabad over ties between the country's intelligence service and militants. The New York Times said agency deputy director Stephen Kappes highlighted alleged ties between Pakistan's Inter-Services Intelligence (ISI) and those responsible for the surge of violence across the border in Afghanistan. "We reject this report. This is unfounded, baseless and malicious," chief Pakistani military spokesman Major General Athar Abbas told AFP. "I would like to emphasise here that ISI is a premier intelligence agency which has caught or apprehended maximum Al-Qaeda operatives including those who were linked with criminals and responsible for attacking the US mainland on September 11, 2001," Abbas said.