Sandy Berger (search) said he made "an honest mistake" but Republicans aren't completely buying that explanation.

The national security adviser under former President Bill Clinton's (search) said he regrets the way he handled classified terrorism documents pertaining to the Sept. 11 commission. Berger told reporters he was not guilty of criminal wrongdoing.

"Last year, when I was in the Archives reviewing documents, I made an honest mistake. It's one that I deeply regret," Berger said late Tuesday. "I dealt with this issue in October 2003 fully and completely. Everything that I have done all along in this process has been for the purpose of aiding and supporting the work of the 9/11 commission, and any suggestion to the contrary is simply, absolutely wrong."

But the GOP says the whole snafu raises questions about whether Berger tried to hide embarrassing materials, since he was reportedly seen stuffing documents down his pants, shirt and in his socks.

"What information could be so embarrassing that a man with decades of experience in handling classified documents would risk being caught pilfering our nation's most sensitive secrets?" House Speaker Dennis Hastert (search), R-Ill., said. "Mr. Berger has a lot of explaining to do."

Others insist it's too early to draw conclusions about the controversy.

"I think it is very, very unfortunate that the matter came into public attention while it's under investigation," Sen. Arlen Specter, R-Pa., told FOX News on Wednesday, adding that Berger is entitled to the presumption of innocence until proven otherwise. "Even if later on, someone is exonerated, you can never remove the stain."

"The timing is suspicious but not conclusive," he added.

White House spokesman Scott McClellan said Wednesday that the Justice Department notified the office of White House legal counsel Alberto Gonzalez about the probe before news of it leaked to the media Monday.

"My understanding is that this investigation has been going on for several months and that some officials in our counsel's office were contacted as part of the investigation," McClellan told reporters. "The counsel's office is the one that is coordinating with the Sept. 11 commission the production of documents and since this relates to some documents, the counsel's office was contacted as part of that investigation."

The Justice Department is investigating whether Berger committed a crime by removing from the National Archives (search) copies of documents about the government's anti-terror efforts and notes that he took on those documents. Berger was reviewing the materials to help determine which Clinton administration documents to provide to the independent commission investigating the Sept. 11, 2001, terror attacks.

When news of the investigation surfaced, Berger on Tuesday quit as an informal adviser to Massachusetts Sen. John Kerry's (search) presidential campaign to limit the political fallout.

Kerry said later, "Sandy Berger is my friend, and he has tirelessly served this nation with honor and distinction. I respect his decision to step aside as an adviser to this campaign until this matter is resolved objectively and fairly."

House GOP Leader: 'Could Be a National Security Crisis'

Many Democrats, including former President Clinton himself, suggested that politics were behind disclosure of the probe only days before Thursday's scheduled release of the Sept. 11 commission report. That report is expected to be highly critical of the government's response to the growing Al Qaeda threat, a potential blow to President Bush's re-election campaign.

"It's interesting timing," Clinton said at a Denver autograph session for his book, "My Life." Berger served as national security adviser for all of Clinton's second term.

Berger and his lawyer, Lanny Breuer, said the former Clinton adviser knowingly removed the handwritten notes by placing them in his jacket and pants and inadvertently took copies of actual classified documents in a leather portfolio. He returned most of the documents, but some still are missing.

House Majority Leader Tom DeLay, R-Texas, told reporters the case was about theft and questioned a statement by Berger issued Monday attributing the removal of the documents and notes to sloppiness.

"I think it's gravely, gravely serious what he did, if he did it. It could be a national security crisis," DeLay said.

Asked to comment on that Wednesday, Breuer said he was "very disappointed with this reaction."

"It was an advertent mistake," he said on NBC's "Today" show. "All I can tell you is that when this matter started a year ago, I said to the Department of Justice that we were going to deal with this in good faith, that we wouldn't go to the press and that we wouldn't make this political .... and then suddenly, days before the 9/11 commission report comes out, this is leaked."

Kerry Letter Points Finger at Cheney, Gillespie

The Kerry campaign released a letter detailing campaign questions as to whether Vice President Dick Cheney and Republican National Committee Chairman Ed Gillespie orchestrated the Berger investigation leak.

The letter entitled "Cheney Strikes Back?" says: "The argument that the timing was politically motivated and coordinated by the White House was just made stronger by some very disturbing reports about Dick Cheney and Ed Gillespie."

It goes on to say Cheney and Gillespie reportedly were seen Tuesday meeting with those Senate Republicans who went on the record after the scandal broke, launching a "scurrilous effort to smear the Kerry campaign" by saying Berger gave Kerry port-security documents, the Democratic presidential campaign's letter states.

"If true, the fact that the White House has Cheney coordinating a political attack at a time when the 9/11 report is coming out with recommendations on how to improve the nation's security speaks volumes about the Bush approach to governing," the letter states.

The documents involved have been a key point of contention between the Clinton and Bush administrations on the question of who responded more forcefully to the threat of Al Qaeda terrorism. Written by former National Security Council aide Richard Clarke, they discuss the 1999 plot to attack U.S. millennium celebrations and offer more than two dozen recommendations for improving the response to Usama bin Laden's Al Qaeda network.

In his April 13 testimony to the Sept. 11 commission, Attorney General John Ashcroft said the review "warns the prior administration of a substantial Al Qaeda network" in the United States. Ashcroft said it also recommends such things as using tougher visa and border controls and prosecutions of immigration violations and minor criminal charges to disrupt terror cells.

"These are the same aggressive, often-criticized law enforcement tactics that we have unleashed for 31 months to stop another Al Qaeda attack," Ashcroft told the panel. He added that he never saw the documents before the Sept. 11 attacks.

Berger said in his March 23 testimony to the commission that Clinton submitted a $300 million supplemental budget to Congress to pay for implementing many of the documents' recommendations. Berger acknowledged, however, that not all of them were accomplished.

In his statement Monday, Berger said that every Clinton administration document requested by the Sept. 11 commission was provided to the panel. Berger also said he returned some classified documents and all his handwritten notes when he was asked about them, except for two or three copies of the millennium report that may have been thrown away.

Al Felzenberg, spokesman for the Sept. 11 commission, said the Berger investigation will have no bearing on the panel's report.

FOX News' Carl Cameron and The Associated Press contributed to this report.