The fighting on Saturday in the Mannar, Vavuniya, Weli Oya and Jaffna areas saw one soldier killed, the ministry said. It also said 25 rebels and 34 soldiers were injured.
The Liberation Tigers of Tamil Eelam (LTTE), however, said that they had killed four soldiers in the Vavuniya area alone.
The rebels did not report on their own losses.
Casualty figures in Sri Lanka cannot be independently verified, as the defence ministry bars journalists from reporting from frontline areas or travelling into the rebel-held north.
The latest defence ministry figures bring to 4,122 the number of rebels killed since the start of the year, when the government pulled out of a Norwegian-brokered truce with the rebels.
The ministry says it has lost only 340 soldiers during the same period.
The Tigers are fighting to carve out an independent homeland for minority Tamils in the island's north and east. Tens of thousands of people have died on both sides in more than 35 years of conflict.