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WASHINGTON — The FBI and Justice Department prosecutors have recommended bringing felony charges against David Petraeus, contending he provided classified information to a lover while he was director of the CIA, officials said, leaving Attorney General Eric Holder to decide whether to seek an indictment that could send the pre-eminent military officer of his generation to prison.

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

FBI agents discovered classified documents on her computer after Petraeus resigned from the CIA in 2012, when the affair became public.

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

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

The process has also frustrated Petraeus’ friends and political allies, who say it is unfair to keep the matter hanging over his head. Sen. John McCain, R-Ariz., wrote to Holder last month that the investigation had deprived the nation of wisdom from one of its most experienced experts.

“At this critical moment in our nation’s security,” he wrote, “Congress and the American people cannot afford to have his voice silenced or curtailed by the shadow of a long-running, unresolved investigation marked by leaks from anonymous sources.”

Since his resignation from the CIA on Nov. 10, 2012, Petraeus has divided his time between teaching, making lucrative speeches and working as a partner in one of the world’s largest private-equity firms, Kohlberg Kravis Roberts.

Holder has said little publicly about the investigation. FBI Director James Comey, asked in December why it was taking so long, said: “I can’t say. I mean, I guess I could say, but I won’t say.”

Marc Raimondi, a Justice Department spokesman, declined to comment on the investigation. Several officials who discussed it did so on the condition of anonymity.

At a news conference shortly after Petraeus resigned, President Obama said he had no evidence that Petraeus had disclosed classified information “that in any way would have had a negative impact on our national security.”

But investigators concluded that, whether the disclosure harmed national security, it amounted to a significant security breach in the office of one of the nation’s most trusted intelligence leaders. They recommended Petraeus face charges, saying lower-ranking officials had been prosecuted for far less.

Federal agents stumbled onto the affair after Jill Kelley, a friend of Petraeus, complained to the FBI that she had received anonymous threatening emails about her relationship with Petraeus. FBI agents opened a cyberstalking investigation, traced the message to Broadwell and began searching her emails. That is when they discovered evidence that she and Petraeus were having an affair.

Petraeus is said to have begun the affair with Broadwell in 2011, soon after taking the job at the CIA and she was interviewing him for her book, “All In: The Education of General David Petraeus.

When he resigned from the CIA, Petraeus admitted to the affair, saying that “after being married for over 37 years, I showed extremely poor judgment.”