"It is reported that four villagers have been killed in the incident," a ministry statement said.
The attack came as the military said they killed three suspected rebels in northern Sri Lanka after the air force bombed guerrilla targets in the northeast.
Security forces shot dead three men who tried to infiltrate the army's defence lines at Muhamalai in the Jaffna peninsula on Wednesday night, they said.
The shooting came hours after the air force bombed what it called the main Sea Tiger headquarters of the LTTE, a claim rejected by the guerrillas.
The LTTE said two civilians were killed and four more were wounded in the aerial bombardment in Mullaitivu district.
A first air raid hit the "White Pigeon" charity which helps victims of landmines, the LTTE said, adding that the civilians died in further aerial bombing in th