The air sorties were carried out over the rebel-held Iranamadu area late on Friday, the ministry said in a statement.
The offensive came hours after a suicide bomber rammed into a police bus in the capital of Colombo, killing 11 people and injuring more than 80.
Troops advancing into rebel-held areas killed at least 16 guerrillas in Vavuniya on Friday, the statement said, without detailing the casualties suffered by government forces.
Friday's fighting brought the number of rebels killed by security forces since the start of the year to 3,716 while 276 soldiers have died in combat during the same period, according to ministry figures.
Casualty numbers cannot be independently verified as Colombo bars journalists and rights groups from travelling to embattled areas.
The government said it had opened investigations into Friday's attack in Colombo's heavily-guarded commercial area of Fort. The toll from the blast rose to 11 overnight.
The area is home to the official residence