The Justice Department investigation stems from an affair Mr. Petraeus had with Paula Broadwell, an Army Reserve officer who was writing his biography, and focuses on whether he gave her access to his C.I.A. email account and other highly classified information.

F.B.I. agents discovered classified documents on her computer after Mr. Petraeus resigned from the C.I.A. in 2012 when the affair became public.

Mr. Petraeus, a retired four-star general who served as commander of American forces in both Iraq and Afghanistan, has said he never provided classified information to Ms. Broadwell, and has indicated to the Justice Department that he has no interest in a plea deal that would spare him an embarrassing trial. A lawyer for Mr. Petraeus, Robert B. Barnett, said Friday he had no comment.

The officials who said that charges had been recommended were briefed on the investigation but asked for anonymity because they were not authorized to discuss it.

Mr. Holder was expected to decide by the end of last year whether to bring charges against Mr. Petraeus, but he has not indicated how he plans to proceed. The delay has frustrated some Justice Department and F.B.I. officials and investigators who have questioned whether Mr. Petraeus has received special treatment at a time Mr. Holder has led a crackdown on government officials who reveal secrets to journalists.