Musharraf denies the interview ever took place
The remarks were said to have been made in a rare sit-down interview at his home over the weekend with USA Today and CBS Radio.
Mr Musharraf is meeting US Secretary of State Colin Powell in Islamabad to discuss Pakistan's role in the war against terror.
The president is alleged to have said he will tell Mr Powell that if Mullah Omar was removed, Osama Bin Laden - America's prime suspect for the 11 September suicide attacks in the US - would be "on the run".
"Get Mullah Omar and Osama won't be able to operate," he is quoted as saying.
Fears for 'guerilla war'
"You must take out the centre of gravity. That is what I would do if I was running this campaign."
He is also reported as saying that the Taleban would not have the strength to effectively fight allied ground forces.
"Either the Taleban will collapse or there will be another 10-year guerrilla war. We will try our best to make sure a guerrilla war does not happen."
Mr Musharraf is said to have clarified comments he made two weeks ago that the US-led attacks on Afghanistan would be over in "a day or two", which contradicted remarks from President George Bush and others that the operation could take some time.
"It could be over in one day if you take out Mullah Omar and his leadership. Once you have done that, the campaign is over. That is what I meant to say."
He is also quoted deriding Islamic militants who have called for a jihad - holy war - against his government and the US.
'Popular leader'
"The people love me. I'm a popular leader wherever I go. Those who are protesting against me are idiots. They don't know anything."
Pakistan Foreign Ministry spokesman Riaz Mohammed Khan said the president had not granted such an interview and no such comments were made.
But Elisa Tinsley, World Editor for USA Today said the interview with their correspondent Jack Kelley did take place.
She said: "We stand by our story. The interview did take place. We have no idea why the foreign ministry is denying it."
A spokeswoman for CBS Radio also said they stood by their story.
They said that over lunch, their reporter Kimberley Dozier asked Mr Musharraf if she could ask some questions on the record, and he said yes.
She took notes, but did not record the interview.