No details were given of losses, but pilots were quoted as saying they had successfully destroyed the artillery positions and a "Sea Tiger base" near Kilinochchi, the LTTE political capital.
However, the Tigers said that the planes had bombed a village.
"Five civilians were killed and seven more were injured, two of them critically, when Sri Lanka bombed a coastal civilian settlement today," the LTTE said.
The Tigers are fighting for independence for Sri Lanka's minority ethnic Tamils concentrated in the north and east of the island.
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The latest raids came after the ministry said 92 Tamil rebels and three government soldiers were killed in battles for a bunker line in the north on Wednesday.
According to the defence ministry, some 1,450 rebels have been killed so far this year. The military es