The accident happened around midday in the remote Gotthard Pass in the Tessin region near a hospice that stands at an altitude of 2,100 metres (6,900 feet).
Emergency services have arrived at the scene, with the number of people travelling in the helicopter unknown.
"There are probably injuries," the ministry said.
At the end of August, a Swiss pilot died after crashing his F/A-18 in the Hinter-Tierberg region, apparently after flight controllers gave him incorrect altitude instructions.
In June, two Swiss Tiger F-5E fighter jets collided in the Netherlands in June during a training flight for an air show.
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.
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