Berger expressed regret over the incident, which he called an "honest mistake."
His decision to quit the Kerry campaign came as both parties sought to use the investigation to gain political advantage or to control damage.
Republicans said the probe raises questions about whether the former Clinton administration official was trying to hide embarrassing materials from the public. Democrats questioned why disclosure of a months-old investigation came just before Thursday's release of the final report by the commission investigating the Sept. 11 attacks.
The report is expected to be highly critical of the government's handling of the pre-Sept. 11 terror threat.
"So is this about Sandy Berger, or is this about politics?" asked Sen. Barbara Mikulski, D-Md.
Former President Clinton also weighed in, telling reporters at a Denver autograph session for his book "My Life" that "it's interesting timing."
Berger served as national security adviser for all of Clinton's second term. "I know him. He's a good man. He worked his heart out for this country," Clinton said.
Speaking to reporters outside his office Tuesday, Berger said: "Last year, when I was in the Archives reviewing documents, I made an honest mistake. It's one that I deeply regret.
"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."
The Justice Department is investigating whether Berger committed a crime by removing from the National Archives 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 Sept. 11 commission.
CBS Chief White House Correspondent John Roberts reports Berger returned to the archives all but two of the documents - which he believes he accidentally threw away. An FBI search of his home in January turned up nothing. And late Tuesday, law enforcement sources say they don't expect charges to be filed.
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. Along with putting documents in his coat and pants, Berger acknowledged removing some documents in a portfolio. He returned most of the documents, but some still are missing.
"That's not sloppy," DeLay said. "I think its gravely, gravely serious what he did, if he did it. It could be a national security crisis."
House Speaker Dennis Hastert, R-Ill., said he was "profoundly troubled" by the allegations, adding that Berger "has a lot of explaining to do."
Lanny Breuer, Berger's attorney, said his client has offered to cooperate with investigators. He said the decision to step aside from the Kerry campaign was done because "Mr. Berger does not want any issue surrounding the 9/11 commission to be used for partisan purposes."
Deputy Attorney General James Comey would not comment on the investigation other than that in general the Justice Department regards takes "very, very seriously" allegations of mishandled classified materials.
"It's our lifeblood, those secrets," Comey said.
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 Osama 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 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 highly anticipated report.
"This is a matter between the government and an individual," Felzenberg said. "They were not our documents, and we believe we have access to all the materials we need to see to do our report."