Soldiers opened fire when hundreds of demonstrators hurled stones at a military jeep in the town of Sittandy, an official said.
"They (the demonstrators) were protesting against the setting up of a combined army-police checkpoint in the area," said the ministry spokesman.
The security forces temporarily dismantled the checkpoint after the shooting sparked more tension in the region, where there has been a spate of killings by rival Tamil rebel factions, local officials said.
The region's top guerrilla leader, V. Muralitharan, better known as Karuna, led an unprecedented split in the Tamil Tiger movement in March last year. Since then there has been a rash of internecine killings.
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Government forces and the main rebel group have been observing an Oslo-brokered truce since February 23, 2002, but dip