The malfunction of pitch rate gyroscopes made the pilot fail to control the plane at take-off, Xinhua news agency reported.
All F-16 jets have four such gyroscopes and simultaneous failure of the gyroscopes is very rare, the Ministry noted.
The Singapore Air Force will undertake further studies to determine the specific cause for the gyroscope malfunction with F-16 producer Lockheed Martin.
Singapore's F-16 fleet will resume flying after checking the pitch rate gyroscopes onboard each jet, the Ministry added.