It said the aircraft "bombed a civilian area with a mechanic workshop", and that Tamil Tiger rebels responded with anti-aircraft fire.
No independent confirmation of the conflicting accounts of the raid was available.
The air strike took place hours after a truce, signed by the LTTE and the government in 2002, officially came to an end at midnight on Wednesday.
It also came a day after the Tigers were blamed for a public-bus bombing in the south which killed 27 civilians and wounded more than 60 others, according to a new toll issued by authorities.
Sri Lanka's troops also claim to have seized a key stretch of road from the LTTE and fought two other battles, killing a total of 23 Tamil Tigers.
The military said on Thursday that soldiers captured a 3km stretch of road connecting Uyilankulam and Adampan villages in northern Mannar district on Wednesday after a battle that killed nine fighters.
Though small, the stretch is seen as strategic in the military's push to take LTTE-held territories in Mannar district, the military said.
The Sri Lankan government pulled out of the ceasefire arguing that the LTTE, which wants to carve out an independent state in the north and east of the island, had only used the truce to re-arm.
Fighting has been escalating over the past year anyway, and Nordic peace monitors said late last year that they had lost count of violations of the Norwegian-brokered ceasefire.
The truce monitors pulled out of Sri Lanka on Wednesday, with a warning to both sides that the long-running war cannot be won.