The military aircraft set off on a routine flight from Payerne airfield in the canton of Vaud on Tuesday at around 8.30am with just one person, an experienced pilot, on board.
It was due to land in Locarno in the canton of Ticino an hour later, but failed to arrive at the expected time.
A search operation was launched and the plane was located at around 4pm on the Schreckhorn in the Bernese Oberland, the army said in a statement.
A recovery operation will commence as soon as the weather permits.
Currently the pilot has not been found.