Air force fighter jets dropped bombs over a rebel supply and storage facility in the guerrilla-controlled northern district of Mullaittvu, the ministry said.
"The enemy target had been under constant surveillance and the latest air reconnaissance information has revealed intensified activities in the area," it said.
Government troops battled the rebels in Mannar district on Saturday, killing 35 Liberation Tigers of Tamil Eelam (LTTE) cadres and wounding 39 guerrillas, the military said.
Eight soldiers died during Saturday's clashes and 13 were injured, the military said.
There was no immediate comment from the LTTE, but the rebels have rejected military casualty claims in the past.
The latest fighting raises the number of rebels killed by security forces since January to 3,376, according to the defence ministry, which says 253 soldiers have died during the same period.
Both sides are known to downplay their own casualty figures and inflate enemy losses. Casualty figures can