The single count is misdemeanor, and Berger reportedly will pay a $10,000 fine.
Berger was reviewing classified documents at the National Archives in July, September and October 2003 while preparing testimony for the National Commission Investigating Terrorist Attacks Upon the United States, known as the "9-11" commission.
He admitted concealing and removing five copies of classified documents from the archives, the Justice Department said. The documents were different versions of a single document.
Berger admitted taking the documents to his Washington office, where he destroyed three of the copies.
Initially, Berger told archives staff he had "accidentally misfiled" two of them. The next day, he returned the two remaining copies of the five documents he had taken during the September and October visits.
Each of the five copies of the document was produced to the commission in due course, the department said.