The Pentagon. (AFP/Getty Images)

A senior Navy intelligence official has been indicted on charges of theft and conspiracy as part of a long-running federal investigation into a secretive military operation featuring the Navy SEALs and untraceable weapons parts.

David W. Landersman, formerly the senior director for intelligence in an obscure Pentagon office that dabbled in covert programs, becomes the third person charged in a mysterious case that has already resulted in two convictions.

Prosecutors charge that Landersman helped arrange a sweetheart $1.6 million defense contract for his brother — a bankrupt California hot-rod mechanic — to manufacture untraceable rifle silencers that turned out to be junk and cost only $10,000 in parts and labor to manufacture.

Other defendants in the case have said the silencers were specially designed for a top-secret military operation involving Navy SEAL Team 6, the elite commando unit that killed Osama bin Laden, and had to be obtained outside normal channels.

Court records show that Landersman, a retired Marine officer, was indicted Sept. 24 by a federal grand jury in Virginia, although the charges were not made public until late Thursday. He was arraigned Friday in U.S. District Court in Alexandria and released on his own recognizance.

“Col. Landersman is an American hero who has won the Silver Star and Bronze Star, and we look forward to him clearing his good name,” Stephen M. Ryan, his attorney, said in an e-mailed statement.

The rifle silencers — 349 of them — were ordered by a Navy intelligence office at the Pentagon known as the Directorate for Plans, Policy, Oversight and Integration, according to charging documents.

Landersman headed the ­civilian-run directorate, which was supposed to provide ­back-office support and oversight for Navy and Marine intelligence operations. But under his leadership, the directorate sometimes became actively involved in secret missions, according to interviews and prior testimony in the case.

Landersman is still employed by the Navy but has been reassigned to a clerical job pending the outcome of the criminal investigation.

Cmdr. William Marks, a Navy spokesman, said Landersman is “no longer performing duties in any way associated with intelligence” and that Navy officials “will consider appropriate administrative action in response to the indictment.”

Landersman was first referred to as a co-conspirator in the case two years ago, but for reasons that remain unclear, he was not charged until this month. The indictment against him contains little information that hasn’t previously been made public.

His brother, Mark S. Landersman, an auto mechanic from Temecula, Calif., was convicted in October 2014 on conspiracy charges for building the untraceable silencers and shipping them across state lines without a proper firearms license.

Also convicted was Lee M. Hall, a civilian Navy intelligence official who worked for David Landersman and helped arrange the delivery. The two men were convicted after a bench trial by U.S. District Judge Leonie M. Brinkema.

In another unexplained twist, after nearly a year, neither has been sentenced, and Brinkema has not issued a written verdict laying out her decision to find them guilty. Attorneys for Hall and Mark Landersman declined to comment.

According to trial testimony, Hall and the Landersman brothers went to unusual lengths to conceal the $1.6 million silencer purchase from other Navy officials and contracting representatives. Three Navy officials said they had approved David Landersman’s request to spend the money on intelligence studies, not a weapons deal.

Although the purpose of the silencers was never established, the trial featured a constant undercurrent of intrigue with carefully couched references to classified projects and black operations. Many filings in the case were placed under seal.