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.