The US is concerned about militants in border areas
The US military says it has evidence elements within Pakistan's military intelligence, the ISI, continue to provide support for the Taleban.
Officials said that this support for militants had to end.
The chairman of the US Joint Chiefs of Staff said the ISI had links with militants on both Pakistan's borders with Afghanistan and India.
US President Barack Obama has announced a new strategy for the "increasingly perilous" situation in Afghanistan.
He said an extra 4,000 US personnel would train and bolster the Afghan army and police, and he would also provide support for civilian development.
Afghan President Hamid Karzai said he was "in full agreement" with the US review.
Two senior figures in the US military have spoken about the links they believe exist between elements in Pakistan's Directorate for Inter-Services Intelligence (ISI) and Taleban and al-Qaeda militants.
People in Islamabad give their views about Mr Obama's speech
"There are certainly indications that's the case," said Admiral Mike Mullen, chairman of the Joint Chiefs of Staff, in a CNN interview.
"Fundamentally that's one of the things that has to change."
In another interview, the head of the US Central Command, General David Petraeus, said some of the militant groups had been established by the ISI and that their links continued.
He said there was evidence that "in the fairly recent past" the ISI had tipped off militants when their positions were in danger.
"It's a topic that is of enormous importance, because if there are links and if those continue and if it undermines the operations [against militants], obviously that would be very damaging to the kind of trust that we need to build," said Gen Petraeus in a PBS interview.
American officials, speaking anonymously to the New York Times, have given more detail.
So I want the American people to understand that we have a clear and focused goal: to disrupt, dismantle and defeat al-Qaeda in Pakistan and Afghanistan
They said the strengthening Taleban campaign in southern Afghanistan was being made possible by military supplies from Pakistan.
The newspaper said electronic surveillance and informants had shown that the level of co-operation was deeper and more extensive than earlier thought.
Pakistani leaders have publically denied any links with the militants.
The BBC's Charles Scanlon says patience in Washington appears to be wearing thin.
On Friday US President Barack Obama said growing radical forces in Afghanistan and the border area in Pakistan posed the greatest threat to the American people and the world.
Pakistani President Asif Ali Zardari said it would strengthen democracy in his country, while the Afghan government said Mr Obama had recognised that the al-Qaeda threat came mainly from Pakistan, and that it was a regional problem.
Zardari defends Pakistan sovereignty
In a speech to parliament on Saturday, Mr Zardari said Pakistan would not allow use of its soil for terrorist activity, and would not let anyone violate its sovereignty.
But he did not specifically criticise US missile attacks on Pakistani territory as he has done in the past.
Cross-border operations by US-led forces have angered Pakistani authorities in recent months.
President Obama said his "comprehensive new strategy" was an outcome of a "careful policy review" in which military commanders and diplomats, regional governments, partners, Nato allies, NGOs and aid organisations were consulted.
US troops carry out joint operations with the new Afghan security forces
He painted a bleak picture of the situation, with insurgents increasing their control of territory in the region around the Afghan-Pakistan border - which he termed "the most dangerous place in the world" for the American people - and attacks rising.
He said American strategy must relate directly to the threat posed to the Americans by al-Qaeda and its allies - who, he reminded his listeners, were behind the 9/11 attacks on American soil eight years ago.
But he said targeting al-Qaeda was not only in the interests of American people, but populations around the world and Afghans themselves.
"This is not simply an American problem. Far from it," Mr Obama said.
"It is instead an international security challenge of the highest order."
In Pakistan, Mr Obama said American help would be needed to go after al-Qaeda, which Mr Obama admitted was "no simple task".
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