The air force hit an "arms and ammunition manufacturing yard" of the Liberation Tigers of Tamil Eelam (LTTE), the ministry said in a statement.
"Sri Lanka air force supersonic fighter jets raided one of the main LTTE arms and ammunition manufacturing yards located in Mullaitivu district this afternoon," the ministry said.
It gave no details of casualties, but said pilots had reported direct hits.
The air attack came a day after fresh ground fighting in the district of Vavuniya left 13 rebels and two soldiers killed, the ministry said.
The latest clashes raises the number of rebels killed by security forces since the start of the year to 4,209, according to defence ministry figures.
A total of 359 soldiers were killed during the same period, it says.
Casualty figures given by both sides vary wildly and cannot be verified independently. The rebels are leading a drawn-out campaign for independence for the island's minority Tamils, who are concentrated in northern and eastern areas.