His remains were identified on Wednesday morning among the wreckage of the plane at the crash site on the Susten Pass, which connects the cantons of Uri and Bern.
“The army sends its sincere condolences to the relatives of the victim,” the ministry said in a statement.
The victim was a 27-year-old air force pilot, it said.
The F/A-18 C single-seater was one of two planes that had just taken off from the Meiringen airbase in the canton of Bern on Monday afternoon when radio contact with the pilot was suddenly cut.
The wreckage of the plane was discovered on Tuesday but the weather conditions and the difficult terrain of the area hampered the search team's rescue efforts.
An investigation has been launched to determine the cause of the crash, said the ministry.
The wreckage of the plane will be removed from the crash site in the coming days, and for the moment the area has been blocked off to hikers.
The air force will resume training exercises on Wednesday afternoon, said the ministry.