Soldiers captured the bases of the Liberation Tigers of Tamil Eelam (LTTE) during an offensive late Friday and early Saturday in the eastern Batticaloa district, the ministry said.
"The army confirms that 30 LTTE terrorists have been killed in the confrontations, including three who had committed suicide in desperation," the ministry said in a statement.
It said one soldier was killed and 17 others were wounded in the battles.
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There was no available comment from the rebels.
Both sides are known to inflate the losses of the other side while playing down their own casualties.
The report came as Japan's special envoy, Yasushi Akashi, was ending a four-day visit to the island Saturday.
He said he was hopeful that the troubled peace process could be salvaged.
The escalating fighting since December 2005 has shattered a 2002 truce brokered by Norway.
Since then, more than 5,000 people have been killed in the ethnic conflict.