The pilot of the Ukrainian-made MiG-27 swing-wing type jet managed to eject to safety before the aircraft crashed into a lagoon, an air force official said.
A similar jet crashed in August 2001, killing its Ukrainian pilot and injuring seven people on the ground after taking off from the same base located next to the country's only international airport.
Both the military base and the airport were attacked by Tamil Tiger guerrillas on July 24, 2001. The rebels destroyed four civilian jets and damaged two more at the airport after gutting eight military aircraft.
A MiG-27 aircraft was lost in the 2001 rebel attack along with two supersonic Israeli-built Kfir ground attack aircraft.
The air force has only carrried out training missions since the government and the rebels entered a Norwegian-brokered truce in February 2002.