Berger is expected to appear in federal court in Washington on Friday, said Justice spokesman Bryan Sierra.
The former Clinton administration official previously acknowledged he removed from the National Archives copies of documents about the government's anti-terror efforts and notes that he took on those documents. He said he was reviewing the materials to help determine which Clinton administration documents to provide to the independent commission investigating the Sept. 11, 2001, terror attacks.
He called the episode "an honest mistake," and denied criminal wrongdoing.
Berger and his lawyer, Lanny Breuer, have said Berger 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.
The charge of unauthorized removal and retention of classified material is a misdemeanor that carries a maximum sentence of a year in prison and up to a $100,000 fine.
The materials related to a 2000 report on how government reacted to the terror threat prior to the millennium celebrations.
Berger stepped down as an adviser to Democratic presidential candidate John Kerry's campaign last July after The Associated Press reported that the Justice Department was investigating the matter.
Many Democrats, including former President Clinton, suggested politics were behind disclosure of the probe only days before the release of the Sept. 11 commission report, which Republicans feared would be a blow to President Bush's re-election campaign.