PORTLAND, Ore. — An F.B.I. agent was found not guilty on Friday of lying to investigators about firing his rifle during a 2016 confrontation when a leader of an armed militia was killed.

The agent, Joseph Astarita, had been accused of firing two shots — neither shot struck anyone — at a roadblock where law enforcement officials were trying to stop leaders of an armed militia that had taken over a federal wildlife refuge in central Oregon.

But the jurors in Federal District Court concluded that Mr. Astarita, 41, a 13-year veteran with the F.B.I. and a member of its elite hostage rescue team, was not the one who fired the mysterious shots. The decision only deepened the mystery that has surrounded the unexplained shots, and has been a topic of intense debate among law-enforcement officials, conspiracy theorists and militia supporters ever since the confrontation along a snowy, tree-lined rural road in central Oregon.

The verdict was seen as a victory for the rescue team whose members said they had felt besieged by the charges against Mr. Astarita. Teammates who had supported Mr. Astarita, believing he had never fired the shots, expressed relief at the outcome. And for the F.B.I., the acquittal was a rare public exoneration in face of relentless attacks by President Trump and his conservative allies.