The accident occurred at about 10.45 a.m. (09:45 GMT) in upper Assam's Tinsukhia district just minutes after the plane had taken off from the Chabua airbase on a training flight, the ministry said. The Indian Air Force has ordered an inquiry into the crash.
The number of accidents involving MiG-21 aircraft has significantly decreased since India began cooperating with Russian experts in 2003 to improve security and pilot safety.
India currently has around 200 MiG-21 planes.