Musharraf said in a US television interview to be broadcast on Sunday that Richard Armitage, the US deputy secretary of state, had told Pakistan's intelligence director to comply with US demands or face being bombed "back into the Stone Age".
However, speaking at a joint press conference with Musharraf on Friday, who is currently on a diplomatic visit to the US capital, Bush said he had never heard of the threat.
"The first I've heard of this is when I read it in the newspaper today.
"I guess I was taken aback by the harshness of the words."
Musharraf responded by saying that he could not discuss his own remarks as, under the terms of a biography book deal he has signed, he cannot comment on such issues until the work is published later this month.
'Caught off guard'
Armitage himself also later denied he had made the alleged comments, saying he had never threatened to use military force and that he was not advised to.
He told the CNN news channel: "I told him that... for Americans, this was black or white, that Pakistan was either with us fully or not.
"It wasn't a matter of being able to negotiate."
He said that his conversation with Mahmood Ahmed, then head of Pakistan's Inter Services Intelligence agency (ISI), was "strong [and] straightforward".
Armitage said: "I think he was looking for a friendly conversation and he got a very straightforward conversation by someone who was saying that the world had changed on 9/11."
Prior to the September 11 attacks Pakistan was one of the few countries to maintain relations with Afghanistan's Taliban government and many Pakistanis were sympathetic with the neighbouring Islamic state.
However, following the attacks, Musharraf cut ties to the Taliban and co-operated with US efforts to track and capture al-Qaeda and Taliban forces that sought refuge in Pakistan, angering many within his own country.