Ground troops clashed with the Liberation Tigers of Tamil Eelam (LTTE) in the northern districts of Vavuniya and Mannar, leaving 43 rebels and five soldiers dead, the ministry said.
Another four rebels were killed further north in the Jaffna peninsula on Saturday.
No independent confirmation of the claim has been made available.
There was no immediate comment from the LTTE, which says it has been fighting for an independent homeland for minority Tamils in the island's north and east since 1972.
Vehicles searched
On Sunday, heavily armed troops and police searched almost all vehicles entering Colombo, a city of almost 650,000 people, causing long traffic delays.
Minority Tamil politicians said hundreds of ethnic Tamils had been detained by the security forces since Saturday as part of the cordon-and-search operations against the rebels.
 |
LTTE chief Prabhakaran has lost a number of
comrades with the war grinding on [GETTY] |
Police said they arrested people who failed to establish their identities in the capital, but declined to say how many had been held for questioning.
Separately, the government has imposed travel restrictions on civilians moving between rebel-held territory in the north and government-controlled areas, Brigadier Udaya Nanayakkara, a military spokesman, said.
Civilians in those areas will be allowed to leave only for medical treatment, prior appointments with government departments and other official business.
Nanayakkara said the move was aimed at preventing rebels from infiltrating the island's south.
The security measure follows twin bomb attacks that rocked the capital last week, leaving 21 dead and more than 40 people wounded.