Heavy fighting in Vavuniya and Weli Oya left 21 rebels dead on Sunday, the ministry said in a statement, putting government casualties at two dead and 10 injured.
In the Mannar district, troops smashed through rebel bunkers on Sunday killing four guerrillas, the ministry said, adding that one soldier was injured during the clashes.
There was no immediate comment from the Liberation Tigers of Tamil Eelam (LTTE), which has been fighting for an independent homeland for minority Tamils since 1972.
However, the pro-rebel Tamilnet.com website reported that the Sri Lankan military pulled back after suffering heavy casualties following six hours of artillery fire in Mannar on Sunday.
The rebels later seized military hardware after troops withdrew, Tamilnet said quoting LTTE local commanders.
Clashes have left 1,779 rebels dead since the start of this year, according to defence ministry figures. The military estimates the Tigers' strength at 5,000 combatants.
Violence has escalated