Major. Mark Thompson faces new charges after The Washington Post uncovered evidence that Thompson was dishonest when he testified before an administrative board. (Nikki Kahn/The Washington Post)

Attorneys for Marine Maj. Mark Thompson on Tuesday questioned the authenticity of a recorded interview that the government intends to use against the former U.S. Naval Academy instructor at his court-martial early next year.

Thompson, 47, has long sought to prove that he was unfairly convicted of sexual misconduct at a 2013 court-martial. The military launched a new investigation into Thompson after The Washington Post uncovered evidence that he was dishonest when he testified under oath to a Marine administrative board.

Thompson now faces new charges of lying to the board, encouraging a friend to lie for him at his court-martial — and lying to a Post reporter about his accusers.

The 45-minute audio recording of The Post’s interview with Thompson, which the newspaper published online in July, is part of the military’s case set to begin in January.

At a preliminary hearing at Marine Corps Base Quantico on Tuesday, Thompson’s attorneys asked a military judge to order The Post to turn over the original recording and contemporaneous notes from the reporter.

“Our contention is that there are portions of the interview missing,” Thompson attorney Kevin B. McDermott said in the courtroom in the basement of Lejeune Hall. “If the government intends to use my client’s statements against him, we believe we should have access to it.”

“We have every right to determine whether the recording is accurate,” he said.

Marine Corps prosecutor Maj. Babu Kaza said The Post had already provided a digital recording of the interview, in addition to a statement from Post counsel, under penalty of perjury, that the recording produced in response to a government subpoena was complete and unaltered.

The notes are irrelevant, Kaza said, because the government does not intend to call reporter John Woodrow Cox as a witness.

McDermott suggested that there was a “sizable gap” in the recording at a critical moment in the interview, and that prosecutors should not be allowed to play the recording at Thompson’s court-martial unless Cox testifies to its authenticity.

During their interview, Cox showed Thompson copies of text messages he uncovered that suggested Thompson was involved in a sexual relationship with a female midshipman. For nearly two minutes, the Marine said nothing, Cox wrote in the story that prompted the new investigation. He described him reading and rereading the text messages as he formulated a response.

The reporter repeatedly asked Thompson in the January interview why he lied to authorities about the last time he saw the woman. Thompson described the immense pressure he faced after another midshipman accused him of raping her.

“I simply had to,” Thompson said in the interview. “When they were coming after me for 41 years” — the sentence he could have faced if he had been convicted of rape — “I can’t begin to say, you know, how terrifying that is.”

Kaza, the prosecutor, said there is no evidence that the recording was altered. The long pause in the recording was intentional on Thompson’s part, Kaza said, because he had just been confronted with “absolute hard evidence of his own lies. It is Mark Thompson spinning his gears to come up with more lies.”

Military Judge Christopher Greer said he would resolve the dispute over the recording in a later ruling. When Thompson’s attorney said he would also seek access to recordings and notes from other interviews The Post conducted with other possible witnesses, the judge cautioned, “The Washington Post is not on trial.”

Thompson, who has spent nearly 20 years in the Marine Corps, including service in Afghanistan, faces charges of making a false official statement and of conduct unbecoming an officer and a gentleman. Military prosecutors have said he should be locked up for nearly three years, fined $200,000 and kicked out of the service.

In addition to the recorded interview with The Post, the government’s case is expected to rely on testimony from Thompson’s friend, Maj. Michael Pretus, who was a key witness for Thompson after then-Midshipman Sarah Stadler accused Thompson of sexual misconduct and a female classmate claimed that he had raped her.

Pretus, a decorated Iraq combat veteran, has since agreed to cooperate with prosecutors as part of an immunity deal. He told investigators that he lied on Thompson’s behalf and also admitted to having a sexual threesome with Thompson and one of his accusers during a visit to Annapolis in 2011, according to a recorded interview played during a military court proceeding in May.

At Tuesday’s hearing, Thompson’s attorneys raised questions about Pretus’s credibility as a witness. McDermott requested any medical records that would show Pretus had received alcohol dependency treatment.

“There is good-faith basis to believe there are significant alcohol issues in this witness’s past and apparently ongoing,” McDermott said.

Pretus declined to comment Tuesday on McDermott’s assertion. He was removed from his position as an instructor at the Naval Academy after being implicated in the sexual misconduct scandal.

At Thompson’s court-martial in 2013, it was Pretus who provided key testimony that contradicted the accusers’ version of events. Thompson was acquitted of the rape but convicted of five other charges related to sexual misconduct.

Pretus told investigators he had not wanted to testify during Thompson’s court-martial but did so out of loyalty to his friend.