The President, who will meet Mr Bush in the White House today, said the threat was made by Richard Armitage, then the Deputy Secretary of State, in the days after the terror attacks, and was issued to the Pakistani intelligence director.

“The intelligence director told me that [Armitage] said, ‘Be prepared to be bombed. Be prepared to go back to the Stone Age’,” President Musharraf said. “I think it was a very rude remark.” The claims come at the end of a week in which relations between the US and Pakistan have sharply deteriorated, and days ahead of the publication of President Musharraf’s memoir, In the Line of Fire, which will be serialised in The Times from Monday.

On Wednesday, President Bush, in an interview with CNN, said that he would not hesitate to authorise immediate American military action inside Pakistan if he had intelligence of Osama bin Laden’s whereabouts. Asked if he would give an order to kill the al-Qaeda leader, Mr Bush said “absolutely”.

President Musharraf was clearly angered by Mr Bush’s declaration that the US would act independently of his authority inside Pakistan.

“We wouldn’t like to allow that. We would like to do that ourselves,” he said. The President’s potentially incendiary claim of US threats comes at a particularly sensitive time between Washington and Islamabad, amid suspicion in Washington that Pakistan is not doing enough to curb a resurgent Taleban in Afghanistan, or in the hunt for bin Laden.

Before the 9/11 attacks Pakistan was one of the only countries in the world to maintain relations with the Taleban, which was harbouring bin Laden, and the Pakistani intelligence services had close relations with the Taleban regime.

In recent days Islamabad has vehemently denied US media reports that it has struck a deal with al-Qaeda and Taleban militants inside Pakistan, and even one report that it has assured bin Laden that if captured, he would not face prosecution. President Musharraf told the CBS 60 Minutes programme that when he was told of Mr Armitage’s threat, he reacted in a responsible way. “One has to think and take actions in the interest of the nation, and that’s what I did,” President Musharraf said.

Documents showed that Mr Armitage, who last night disputed the language but did not deny the claim, met the Pakistani Ambassador and the visiting head of Pakistan’s military intelligence service in Washington on September 13, 2001, and asked Pakistan to take seven steps.

President Musharraf told CBS that he was irked by US demands that Pakistan turn over its border posts and bases for the American military to use.

He said some demands were ludicrous, including one insisting that he suppress domestic expression of support for terrorism against the United States. “If somebody’s expressing views, we cannot curb the expression of views,” he said.

The official 9/11 commission report on the attacks, based largely on government documents, said that US national security officials focused immediately on securing Pakistani co-operation as they planned a response.

Within days of 9/11 President Musharraf cut his government’s ties to the Taleban regime in Afghanistan and co- operated with US efforts to track and capture al-Qaeda and Taleban forces that sought refuge in Pakistan. President Bush often praises Islamabad for being one of Washington’s greatest and most crucial allies in the war on terrorism.

President Musharraf also spoke about his embarrassment when informed at the UN in 2003 by George Tenet, who was then CIA Director, that Pakistani nuclear weapon technology had been passed to Iran and North Korea by the father of the Pakistani nuclear bomb, A. Q. Khan.

“[Tenet] took his briefcase out, passed me some papers. It was a centrifuge design with all its numbers and signatures of Pakistan. It was the most embarrassing moment,” President Musharraf told CBS.

He learnt then, he says, that not only were blueprints being given to Iran and North Korea, but that the centrifuges themselves — the crucial technology needed to enrich uranium to weapons grade — were being passed to them.

“[Khan] gave them centrifuge designs. He gave them centrifuge parts. He gave them centrifuges.

“[The shipments] were not done once. They must have been transported many times.”

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