The F/A-18 C single-seater had been taking part in a training exercise with a second plane when all radio contact with the pilot was suddenly cut at 4:05pm, the ministry said in a statement.
“Since then, he has been declared missing,” it said.
The suspected crash site is in the area around the Susten Pass in the centre of Switzerland, and is very difficult to access, the ministry said.
Two helicopters had initially taken part in the search, but as night fell and weather conditions worsened they were forced to land.
The ministry said they would resume their flights as soon as the weather permitted, and that in the meantime, two ground crews of rescue workers and mountaineering experts were continuing the search.
“The military command's thoughts are with the pilot's family,” it said, adding that an investigation had been launched.
No details have been released about the pilot. Asked by the media about the pilot's chances of survival, air force chief Aldo Schellenberg said “We maintain hope and pray for him”, reported news agency ATS.
All flights from the Meiringen airbase in the central canton of Bern, where the missing plane had taken off from, had been grounded until noon on Tuesday, said the ministry.
The suspected accident would be the latest in a string of crashes to befall the Swiss airforce.
In June, two Swiss Tiger F-5E fighter jets collided during a training flight for an air show in the Netherlands.
One of the aircraft crashed and burst into flames, but the pilot ejected to safety.
And during another training exercise in October last year, an F/A-18 crashed in an uninhabited part of France's eastern Doubs region.
No one was hurt on the ground and the pilot was only slightly injured after ejecting from the plane.
The last deadly fighter jet crash in Switzerland happened in 2013, when a Swiss F/A-18 two-seater slammed into a mountainside in the centre of the country.
The pilot and his passenger, an air force doctor taking part in a training exercise, were both killed.
Another of the Swiss Hornets crashed in Crans-Montana in the south of the country in 1998, killing both pilots.
Following the accidents, only 30 of Switzerland's original fleet of 34 F/A-18s remain, reported ATS.