Security forces killed the rebels during artillery duels in Jaffna, Weli Oya, Mannar and Vavuniya on Wednesday, the ministry said, adding that two soldiers were wounded.
The government's casualty claims could not be verified and there was no immediate comment from the Liberation Tigers of Tamil Eelam (LTTE), who control a swathe of territory in the island's north.
The government claims it has killed 2,212 rebels since January against the loss of 130 of it own troops.
Both sides are known to offer wildly fluctuating claims that cannot be independently verified as the government prevents reporters and rights groups from visiting frontline areas.
Tens of thousands have died since the LTTE launched a separatist campaign in 1972 to carve out an independent homeland for minority Tamils in the island's north and east.
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