WASHINGTON — A member of the F.B.I.‘s elite Hostage Rescue Team involved in a deadly confrontation last year with a prominent antigovernment protester in Oregon has been indicted on charges of lying and obstruction, according to federal court documents.
The indictment of the agent, Joseph Astarita, 40, is a blow to the reputation of the hostage team, which carries out the bureau’s riskiest missions in the United States and abroad.
Mr. Astarita was accused of lying to supervisors about firing his weapon in the effort to arrest Robert Finicum, known as LaVoy, who was killed during a standoff at a remote federal wildlife refuge in January 2016. Mr. Finicum led a small band of armed militants who said that the federal land had been improperly taken from area ranchers and demanded that it be returned to local or private control.
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Mr. Astarita pleaded not guilty to all five counts on Wednesday in Portland, Ore., and was released pending court appearances. An F.B.I. spokesman declined to discuss the case but said Mr. Astarita had been assigned to administrative duty.
The case was being investigated by the Justice Department’s inspector general along with federal prosecutors in Oregon.
Mr. Finicum was protesting at the Malheur Federal Wildlife Refuge near Burns, Ore., on Jan. 2, 2016, where the show of defiance led to a lengthy standoff with the F.B.I. and the local authorities.
When Mr. Finicum left the refuge to attend a nearby meeting several weeks later, Oregon state troopers and several members of the F.B.I. team tried to stop his truck and another vehicle. After Mr. Finicum’s truck crashed into a snowbank, he fled and he was shot by state troopers after it appeared he tried to reach for a gun.
Local investigators determined that the shooting was justified but suspected that one of the F.B.I. agents had tried to cover up whether he had fired any shots. The bullet casings were never recovered.
Video footage recorded by a passenger in Mr. Finicum’s truck showed that two shots were fired after Mr. Finicum stepped out of the vehicle, one shattering its window. The authorities said the only person who could have fired those shots — based on an analysis of surveillance videos and photographs — was an F.B.I. agent.
Six rounds were fired by the state troopers, and two by the F.B.I., the investigators found. Three rounds struck Mr. Finicum, 54.
Prosecutors accused Mr. Astarita of misleading the Oregon authorities who were investigating the shooting.
Former team members remained perplexed about why Mr. Astarita would not acknowledge firing the rounds if he had done so. At worst, they said, he might have been kicked off the team and reassigned. They said Mr. Astarita was relatively new to the team when he was deployed to Oregon.
The Hostage Rescue Team was formed in 1983. Its members go through exhaustive training, working closely with military commando units such as the Navy SEALs and the Army’s Delta Force in Iraq and Afghanistan. The unit participated in the arrests of terrorists in Libya in 2014, including a suspect in the attack on a United States diplomatic compound in Benghazi.
In recent years, the team has been involved in a number of rescue operations in Alabama, Idaho and Georgia. But the unit has also been associated with the deadly raids in the 1990s in Waco, Tex., and in Ruby Ridge, Idaho.
Correction: June 28, 2017
An earlier version of this article reported that the Hostage Rescue Team was formed in 1972. It actually was formed in 1983.