Cracks were also discovered in another six F-5 planes,which will be repaired between now and the first quarter of 2016, the department said.
A fissure in the supporting structure of one of the air force’s F-5E Tiger planes was first noticed in 2014.
A larger crack was noted in the airframe of a second plane in January 2015 leading to a detailed examination of all the 36 F-5 Tiger aircraft that were flying regularly.
This led to the detection of “serious” fissures in a total of 16 planes.
Between 1978 and 1984 the Swiss Air Force acquired 110 F-5 Tiger planes (98 singe-seater models and 12 two-seaters) produced by the American aircraft manufacturer Northrop Corporation, which merged with Grumman in 1994 to become Northrop Grumman.
Today, the force is flying just 26 of the fighter jets after most of them were earlier retired from service.
One of the impacts of the downsized fleet is that the Patrouille Suisse, the air force’s aerobatic team, will not always be able to fly six planes, the defence department said.
In May last year, Swiss voters rejected a government plan to buy 22 Gripen fighter jets from Swedish company Saab for 3.1 billion francs as part of a plan to replace the F-5 Tiger planes.
The F-5 Tiger fleet was to have been completely withdrawn from service by next year.
The Swiss Air Force also has 32 Boeing F/A-18 Hornets in its combat fleet.
Defence Minister Ueli Maurer has acknowledged that the Gripen decision has created “security gaps” for the force that need to be addressed.