Pettitte disclosed the conversation to the congressional committee holding Wednesday's hearings on drug use in baseball, according to multiple media outlets.
A person familiar with the affidavit, who said it was signed Friday night, told The Associated Press that Pettitte also said Clemens backtracked when the subject of HGH came up again in conversation in 2005, before the same House committee held the first hearing on steroids in baseball. The person spoke on the condition of anonymity because the affidavit had not been released.
Pettitte said in the affidavit that he asked Clemens in 2005 what he would do if asked by the media about HGH, given his admission years earlier. According to the account told to the AP, the affidavit said Clemens responded by saying Pettitte misunderstood the previous exchange in 1999 or 2000 and that, in fact, Clemens had been talking about HGH use by his wife in the original conversation.
"We don't know what Andy said," Clemens' lead lawyer, Rusty Hardin, said in a statement e-mailed to the AP by his spokesman. "We look forward to hearing tomorrow."
The existence of the affidavit first was reported by The New York Times. The details of its contents was first reported by the AP.
This information came after a source close to Rep. Tom Davis, R-Va., told ESPN.com's T.J. Quinn that the congressman says he was misquoted and misunderstood in a published report about Pettitte's deposition.
Appearing on ESPN's "Outside The Lines," Davis wouldn't directly address the details contained in the Newsday report but said that Pettitte's affidavit "doesn't get into a lot of detail."
"His entire deposition eventually will speak for him. He does have an affidavit that probably will be in the record [Wednesday]."
Davis said that Pettitte wasn't needed at Wednesday's hearing.
"No ballplayer in their right mind wants to come up before a congressional committee. It wasn't like he could add anything," Davis said.
Davis said the reason that Clemens was asked to testify Wednesday is "because he said the Mitchell report was wrong. ... The report has a lot of credibility with Congress and if there is anything that takes away from that, we need to understand what it is."
The report in Newsday said Pettitte's affidavit helps to support Brian McNamee's version of events that the former trainer gave Clemens steroids and HGH, Davis told Newsday in the now-disputed account.
Although Pettitte won't testify at Wednesday's hearings, the left-hander's affidavit will be presented to Clemens at the hearing and will be part of the public record, the newspaper reported.
The Newsday report stated that Davis told the newspaper that Clemens says in his affidavit that both Pettitte and McNamee are mistaken in their statements.
Newsday, citing confidential sources, reported that during a workout in 2002, Pettitte asked McNamee: "How come you don't give me the stuff you give Roger?" McNamee reportedly replied "Because it's illegal."
Clemens, however, says in his affidavit that Pettitte was mistaken in thinking that the conversation was about steroids or HGH, Newsday reported.
Clemens does not attack Pettitte in his affidavit, Newsday reported.
McNamee has accused Pettitte of using human growth hormone -- something Pettitte acknowledged he did do for two days in 2002 to deal with an elbow injury. Before Pettitte spoke to committee lawyers under oath last week, Earl Ward, an attorney for McNamee, said he thought Pettitte would tell the House Committee on Oversight and Government Reform he discussed HGH with Clemens between the 2001 and 2002 seasons.
Clemens has vehemently denied ever using performance-enhancing drugs.
Rusty Hardin, who is Clemens' lead attorney, told Quinn that it was "completely understandable" that Pettitte wouldn't want to appear in a hearing. "Who would?" he said.
Asked whether Pettitte's desire to skip the hearing was a sign that his testimony was incriminating to Clemens, Hardin said, "it would be a huge mistake to assume that."
Hardin said Clemens "has always welcomed Andy's participation" and that he plans "to testify fully and truthfully as he always has."
In an interview that appeared in Tuesday's New York Times, Hardin criticized Rep. Henry Waxman.
"You have a chairman who is going down the tubes because his own committee doesn't support what he is doing," Hardin told the Times in a telephone interview.
On Sunday, Waxman sent a letter to Hardin, saying that some comments by Hardin and McNamee's lawyers were "inadvisable." Hardin told the Times on Saturday that it would be "brazen" and "unbelievable" if IRS Special Agent Jeff Novitzky, a key prosecutor in the BALCO drug cases, attends the hearing.
"If he ever messes with Roger, Roger will eat his lunch," Hardin was quoted as saying.
"I do not know your intent in making this statement, but under one interpretation it can be seen an attempt to intimidate a federal law enforcement official in the performance of his official duties," Waxman wrote. "It is not your client's prerogative to dictate who attends or does not attend the hearing. ... I trust you did not intend your comments to be a signal that there could be adverse repercussions to a federal law enforcement official for attending the hearing or taking other official actions."
Wednesday's session, which will focus on allegations made in the Mitchell report by McNamee that he injected Clemens more than a dozen times with performance enhancers, had been expected to include five witnesses testifying -- Clemens, Pettitte, Chuck Knoblauch, McNamee and Kirk Radomski.
The only people now scheduled to testify on Wednesday are Clemens, McNamee and Charlie Scheeler of former Senate majority leader George Mitchell's staff.
Clemens' wife Debbie, who McNamee said he injected with HGH prior to a Sports Illustrated swimsuit issue photo shoot in 2003, will also attend the hearings.
Sources told Quinn that Pettitte was not a good witness when he appeared before congressional lawyers during a sworn deposition on Monday. Pettitte often contradicted himself, the sources said, so the committee agreed to his request not to appear Wednesday.
Lawyers familiar with the hearings would not say if Pettitte implicated Clemens as a steroids user in his testimony. However, they said that Pettitte's testimony didn't fully jibe with Clemens' versions of events.
Information from The Associated Press was used in this report.