In a radio interview, Armitage, who was then deputy secretary of state, also said Musharraf had fired the intelligence director shortly after he had relayed the alleged U.S. threat to the Pakistani president.
Musharraf said in an that Armitage told a Pakistani official the United States would attack Pakistan if it didn't back the war on terror.
"The intelligence director told me that (Armitage) said, 'Be prepared to go back to the Stone Age,'" Musharraf said.
Armitage has disputed the language attributed to him but did not deny the message was a strong one.
"It did not happen. I was not authorized to say something like that. I did not say it," Armitage said Friday in an Associated Press Radio interview.
Armitage — who was former Secretary of State Colin Powell's right-hand man at the time — said he called the State Department Friday morning to double-check his memory and had an employee read him the cable he had sent after his meeting with the Pakistani intelligence chief, whom Armitage identified as Gen. M.
"I reviewed the cable, or had it read to me this morning from the State Department, and there was in no way that threat," Armitage said.
The exchange occurred during the lead-up to the U.S.-led invasion of Afghanistan to flush al Qaeda fighters out of their bases and to capture or kill Osama bin Laden and his chief lieutenants. Bin Laden and al Qaeda's No. 2 man, Ayman al-Zawahiri, remain at large.
"I told him in a very straightforward way this was a black-and-white issue for Americans. You were either for us or against us.
"He started to tell me about Pakistan's history. ... I said, 'You should communicate with your president and see if you are willing to cooperate with us.'"
He said he told Gen. M that if the answer was yes, they could meet the next day and Armitage would tell him the U.S. requirements. "They will be onerous," he said he told the Pakistani.
"The general came back the next day and said they were willing to go along with us. And I presented to him a list of items Secretary Powell and I had jotted down the night before."
He said several State Department personnel were in the room and heard the exchange, and "no one remembers a military threat. And the cable does not reflect that."
"I would note that Gen. M was fired not long after that by President Musharraf," Armitage added.
Armitage said he met with Musharraf on Thursday. He did not discuss their conversation.
Julie Reside, a State Department spokeswoman, said she knew no specifics of the Armitage documents, but department cables generally reflect conversations precisely.
Earlier Friday, President Bush by Musharraf's comments. At a joint White House news conference, Mr. Bush praised Musharraf for being one of the first foreign leaders to come out after the Sept. 11, 2001.
Musharraf wouldn't comment on his statement, saying he has a book coming out and that he's promised the publisher he wouldn't talk about it.
Mr. Bush accepted that answer and told reporters to "buy the book," CBS News White House correspondent Mark Knoller reports. Musharraf's book will be published by Simon & Schuster, which is part of CBS Corp.
As for Musharraf, no matter how his relationship with the United States was started, a senior White House official said President Bush trusts him fully as a partner in the hunt for Osama bin Laden, reports CBS News White House correspondent Jim Axelrod.