US President George W Bush has said he was "taken aback" by allegations by Pakistan's president that the US threatened to bomb Pakistan in 2001.
In a joint press conference after the two leaders met at the White House, Mr Bush said the first he had heard of the issue was in the day's media reports.
Mr Bush and President Pervez Musharraf emphasised their trust in each other.
Gen Musharraf stressed the importance of the Palestinian issue, saying it was at the heart of terror and extremism.
In excepts from an interview with CBS released on Thursday, Gen Musharraf said the US had threatened to bomb Pakistan "back to the Stone Age" unless it joined the fight against al-Qaeda.
He said the warning had been delivered by former Deputy Secretary of State Richard Armitage to Pakistan's intelligence director.
Mr Armitage told the BBC he had told Gen Musharraf on Thursday: "I would never say that. I don't command aircraft and I didn't have the authorisation."
He confirmed he had held a conversation with the Pakistani general Mr Musharraf had sourced the comments to, but said had not threatened military action.
At the press conference, where Mr Bush spoke first, the US president said he knew of no such conversation.
In his response to a reporter's question on the subject, the Pakistani president said, to laughter, that he was "honour-bound" with his publisher not to discuss details of his autobiography due out next week.
Some analysts say the timing of his comments on CBS may be an attempt to generate interest in the book.
The BBC's Jonathan Beale in Washington says that, in the CBS interview, Gen Musharraf was deliberately distancing himself from the White House in the face of intense pressure within Pakistan over his close ties to Washington.
Correspondents say the Pakistani leader's comments are likely to be believed by many people within Pakistan and increase anti-American feelings there.
Pakistan's support was considered crucial in the defeat of Afghanistan's Taleban government, which Pakistan had helped to bring to power.
Gen Musharraf said the two leaders had also discussed the need for a resolution to the Israeli-Palestinian conflict.
He said he was "extremely glad" the US president "had a desire and a will" to resolve the dispute.
Gen Musharraf defended a deal to halt militant activity near the border
The Pakistani leader also said a recent peace agreement between his government and tribes along the Pakistan-Afghanistan border was not a deal with the Taleban, as suggested by media reports.
"This deal is against the Taleban. This deal is with the tribal elders," Mr Musharraf said.
The two leaders presented a united front when questioned over apparent differences over how Osama Bin Laden would be caught if he was tracked down.
Mr Bush on Wednesday told CNN television he would send US troops into Pakistan if intelligence located al-Qaeda leaders there.
However American soldiers are not officially allowed to operate on Pakistani soil and at a press conference the same day, Gen Musharraf said: "We would like to do it ourselves."
In Friday's press conference, however, both leaders stressed that they were "on the hunt together".
The US president, General Musharraf and Afghan President Hamid Karzai are due to meet next week.