Former President Clinton's national security adviser is under criminal investigation for taking highly classified terrorism documents that should have been turned over to the independent commission probing the Sept. 11, 2001, terror attacks, FOX News has confirmed.

Sandy Berger (search) is under scrutiny by the Justice Department (search) following the disappearance of documents he was reviewing at the National Archives.

Berger's home and office were searched earlier this year by FBI (search) agents armed with warrants after the former Clinton adviser voluntarily returned some sensitive documents to the National Archives (search) and admitted he also removed handwritten notes he had made while reviewing the sensitive documents.

However, some drafts of a sensitive after-action report on the Clinton administration's handling of Al Qaeda terror threats during the December 1999 millennium celebration are still missing, officials and lawyers said. Officials said the missing documents also identified America's terror vulnerabilities at airports to seaports.

• Click to read Berger's testimony before the Sept. 11 commission (pdf file).

Berger and his lawyer said Monday night he knowingly removed the handwritten notes by placing them in his jacket, pants and socks, and also inadvertently took copies of actual classified documents in a leather portfolio.

"I deeply regret the sloppiness involved, but I had no intention of withholding documents from the commission, and to the contrary, to my knowledge, every document requested by the commission from the Clinton administration was produced," Berger said in a statement.

There are laws strictly governing the handling of classified information, including prohibiting unauthorized removal or release of such information.

Lanny Breuer, one of Berger's attorneys, said his client had offered to cooperate fully with the investigation but had not yet been interviewed by the FBI or prosecutors.

Berger served as Clinton's national security adviser for all of the president's second term and most recently has been informally advising Democratic presidential candidate John Kerry. Clinton asked Berger last year to review and select the administration documents that would be turned over to the Sept. 11 commission.

Late Tuesday, Berger announced that he would no longer aid Kerry's presidential bid, saying he didn't want to diminish the work of the Sept. 11 commission.

"Mr. Berger does not want any issue surrounding the 9/11 commission to be used for partisan purposes. With that in mind he has decided to step aside as an informal adviser to the Kerry campaign until this matter is resolved," Breuer said.

Deputy Attorney General James Comey told reporters Tuesday he could not comment on the Berger investigation but did address the general issue of mishandling classified documents.

"As a general matter, we take issues of classified information very seriously," Comey said in response to a reporter's question about the Berger bind, adding that the department has prosecuted and sought administrative sanctions against people for mishandling classified information.

"It's our lifeblood, those secrets," Comey continued. "It's against the law for anyone to intentionally mishandle classified documents either by taking it to give to somebody else or by mishandling it in a way that is outside the government regulations."

'Inadvertent' Action?

The FBI searches of Berger's home and office occurred after National Archives employees said they believed they witnessed Berger placing documents in his clothing while reviewing sensitive Clinton administration papers and that some documents were missing.

Berger said he returned some classified documents that he found in his office and all of the handwritten notes he had taken from the secure room, but could not locate two or three copies of the millennium terror report.

"In the course of reviewing over several days thousands of pages of documents on behalf of the Clinton administration in connection with requests by the Sept. 11 commission, I inadvertently took a few documents from the Archives," Berger said.

"When I was informed by the Archives that there were documents missing, I immediately returned everything I had except for a few documents that I apparently had accidentally discarded."

Breuer said Berger believed he was looking at copies of the classified documents, not originals.

Government and congressional officials said no decision has been made on whether Berger should face criminal charges.

Although lawmakers didn't want to make a judgment call on Berger's fate until all the facts are known, they agreed that the situation doesn't look good for Berger, or even for Kerry.

"There's an ethic here -- that is of strict discipline, of not letting the fact you're working on a political campaign start to color your actions when it comes to national security," Rep. Duncan Hunter, R-Calif., told FOX News on Tuesday.

Sen. Joe Lieberman, D-Conn., called the news "surprising" and said that "unless we learn otherwise, I have to assume that what Sandy said was right -- that any removal of documents was inadvertent. But it is serious."

Sen. Trent Lott, R-Miss., said, "we need more information -- obviously the timing of it is not good" for Kerry.

"From now on, until the election, everything like this will have a spotlight put on it, examined very carefully," Lott continued.

More 'Innocent Than It Looks?'

David Gergen, who was an adviser to Clinton and worked with Berger for a time in the White House, said Tuesday, "I think it's more innocent than it looks."

"I have known Sandy Berger for a long time," Gergen said in a television interview. "He would never do anything to compromise the security of the United States." Gergen said he thought that "it is suspicious" that word of the investigation of Berger would emerge just as the Sept. 11 commission is about to release its report, since "this investigation started months ago."

Berger testified publicly at one of the commission's hearings about the Clinton administration's approach to fighting terrorism.

Berger had ordered his counterterrorism adviser, Richard Clarke, in early 2000 to write the after-action report and has publicly spoken about how the review brought to the forefront the realization that Al Qaeda had reached America's shores and required more attention.

The missing documents involve two or three draft versions of the report as it was being refined by the Clinton administration. The Archives is believed to have copies of some of the missing documents.

In the FBI search of his office, Berger also was found in possession of a small number of classified note cards containing his handwritten notes from the Middle East peace talks during the 1990s, but those are not a focal point of the current criminal probe, according to officials and lawyers.

Breuer said the Archives staff first raised concerns with Berger during an Oct. 2 review of documents that at least one copy of the post-millennium report he had reviewed earlier was missing. Berger was given a second copy that day, Breuer said.

Officials said Archive staff specially marked the documents and when the new copy and others disappeared, Archive officials called Clinton attorney Bruce Lindsey.

Berger immediately returned all the notes he had taken, and conducted a search and located two copies of the classified documents on a messy desk in his office, Breuer said. An Archives official came to Berger's home to collect those documents but Berger couldn't locate the other missing copies, the lawyer said.

Breuer said Berger was allowed to take handwritten notes but also knew that taking his own notes out of the secure reading room was a "technical violation of Archive procedures, but it is not all clear to us this represents a violation of the law."

Justice officials have informed the Sept. 11 commission of the Berger incident and the nature of the documents in case commissioners had any concerns, officials said. The commission is expected to release its final report on Thursday.

FOX News' Major Garrett, Liza Porteus, Anna Stolley and The Associated Press contributed to this report.