The sporadic clashes took place around the embattled Vavuniya and Mannar district on Monday, the ministry said, but did not give casualty figures for its own troops.
Elsewhere, the military accused the rebels of gunning down a senior advisor to an ethnic Tamil cabinet minister, Douglas Devananda, in the war-ravaged northern town of Jaffna late Tuesday.
Maheswari Velayudan, who was also a human rights lawyer, was visiting her sick mother when she was shot dead.
An ethnic Tamil businessman was also gunned down in Jaffna late Monday, the ministry said, blaming the attack on the Liberation Tigers of Tamil Eelam (LTTE).
Meanwhile, a policeman was killed and another wounded in a shootout at the eastern lagoon district of Batticaloa on Monday the military said, blaming the attack on the rebels.
There was no immediate comment from the LTTE, who have been locked in armed combat with the Colombo-based government in seeking autonomy in the island's north and east.
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