It did not give details of casualties or damage but said a rebel coordination centre in Mannar on the northwest coast was hit.
The air attacks are part of an escalation of operations by the government, which pulled out of a Norwegian-brokered truce with the ethnic guerrillas last month.
"This (rebel centre) was located in the jungle and was a threat to the current army operations in Vavuniya and Mannar districts," the ministry said in a statement.
There was no immediate comment from the Liberation Tigers of Tamil Eelam (LTTE), but the rebels said a raid on Thursday against the guerrilla stronghold of Mullaittivu in the northeast wounded five civilians.
At least 1,248 rebels have been killed by security forces this year, according to the island's defence ministry, which has placed government losses at 70 soldiers and police.
Both sides are known to offer wildly different casualty claims that cannot be independently verified as journalists and human rights workers are barred from f