The government accused Capt. Joseph Schweitzer of destroying a videotape he shot before his radar-jamming EA-6B Prowler hit the gondola cable during a low-level training flight in February 1998.
All 20 people aboard the gondola were killed.
Schweitzer admitted to the military judge, Col. Alvin Keller, that he made a mistake by throwing the tape into a fire two days after the flight.
"It was a stupid thing to do and I regret that," he said. "It was a rash decision."
But Schweitzer said he had stopped taping about 10 minutes before the jet flew into the Alpine valley where the accident took place.
"The video had nothing to do with the mishap," Schweitzer said. "It wasn't on in the valley. I didn't want it to be an issue."
Schweitzer also said he and the jet's pilot, Capt. Richard Ashby, never watched the videotape before Schweitzer destroyed it. He said one of the reasons he wanted to destroy the tape was that, at one point during the flight, he turned the camera on his own face and smiled.
Keller accepted Schweitzer's plea Monday afternoon.
"Joe is the type of guy who wants to stand up and take responsibility," said Dave Beck, Schweitzer's civilian attorney, in an interview before the hearing. "There were some bad mistakes made after the accident and they made bad decisions."
A military jury at Camp Lejeune acquitted Ashby of manslaughter and other charges March 4.
Manslaughter counts against Schweitzer were dismissed after Ashby's acquittal. But both faced obstruction of justice and conspiracy charges because of the videotape's disappearance.
A sentence for Schweitzer wasn't immediately clear, but each charge carries a maximum five-years in prison.
Ashby testified during his trial that Schweitzer filmed the early part of their training flight. After they landed, he gave the tape to Schweitzer and said he never saw it again.
Two rear-seat crewmembers were charged in the accident but those charges were dismissed for lack of evidence.
The president of the Italian province where the accident occurred welcomed the plea. "I appreciate Schweitzer's honesty," said Lorenzo Dellai, president of the Province of Trento. "It is a contribution to clearness, which has always been lacking in this sad story."