"The counter terrorist offensive continues with the military battling through stiff LTTE resistance and inter monsoon rains," the ministry said in a statement.
"Troops claimed seizing control over several LTTE bunkers and trenches during Wednesday's fighting," the statement added.
It did not give details of casualties in the latest fighting but said troops recovered two decomposed bodies of Tiger rebels.
Defence ministry maps show that troops are about 10 to 15 kilometres (six to 10 miles) southwest of Kilinochchi.
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The military claims came a day after the Tigers attacked two merchant vessels off the island's northern peninsula of Jaffna using three boats packed with explosives.
Defence officials said the two merchant vessels were salvaged but it was not clear if