Air force fighter jets pounded a "logistics base and combat vehicle conversion plant" in Mullaitivu district early Sunday, the ministry said.
"Pilots confirm that the target was successfully engaged on accurate military intelligence and the entire terrorist complex was on fire after the air strike," the ministry said in a statement.
However, the rebel Liberation Tigers of Tamil Eelam (LTTE) said Sri Lankan jets had killed two civilians and wounded 11 more in the Sunday morning attack.
"Two civilians were killed by an aerial bombing of the Sri Lankan air force on Sunday in Puthukkuriruppu town centre (in Mullaitivu district)," the Tigers said in a statement.
"Eleven civilians were injured.
Several homes and other buildings were damaged in the bombing.
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The government insists it now has the upper hand in the 36-year conflict with the Tigers, who are fighting for a separate Tamil homeland in the majority Sinhalese island's north and east.
On Saturday, security forces captured th