Military spokesman Brigadier Prasad Samarasinghe confirmed the air strikes on Wednesday, but denied they had targeted civilian areas.
Two civilians were reportedly injured.
The raid came just hours after a Tiger attack on a navy base in the tourist city of Galle, which killed one navy sailor and at least 10 Tamil Tiger fighters, a navy spokesman said.
The spokesman said: "They came in three boats and we blew up all three of them. Two small crafts of the navy were damaged in the fighting."
According to the the same source, the Tiger boats sneaked into the base hiding between fishing boats in the adjoining harbour before attacking naval facilities.
"One sailor was killed, 11 wounded and one missing in the fierce fighting that followed," a senior military official said.
Five Tamil boats
The Tamilnet.com website said that a group of 15 Tamil Tigers in five boats carried out the attack.
The separatists used three boats laden with explosives to ram vessels of the Sri Lanka navy, Tamilnet said, adding the other two rebel boats landed and launched attacks against the navy.
Police said they believed four or five fighters had escaped alive.
Galle in the south is far from the
Tigers' base in the northeast
The attack on the navy is the second in three days. Nearly 100 people, mostly sailors, were killed when a Tiger rebel detonated a bomb killing himself and those on a naval convoy in a north-central district on Monday.
Attacks have been spreading throughout the country far from the northern and eastern Tamil strongholds where much of the violence has been concentrated. Galle is located about 113km south of the capital, Colombo.
A riot broke out in the town after the attack according to local police reports and residents. A police curfew was immediately put into place after the 7.45am attack.
Criminal gangs attacked shops belonging to the minority Tamil community in Galle before the police fired into the air to disperse the crowds.
The raid came a day after the government and the Liberation Tigers of Tamil Eelam (LTTE) reiterated their commitment to planned peace talks in Geneva on October 28 and 29.
Few expect the talks to achieve a breakthrough in the face of continued fighting and deep distrust. Hundreds of people have been killed in spiralling violence since late July that shattered a truce brokered in 2002.
The ongoing fighting has left thousands of Sri Lankans displaced and living in camps afraid to go home as fighting has continued on the island.
Last week, dozens of troops and rebels were killed and hundreds wounded in one of the deadliest battles since the truce.
Fuelling the fight
The Sri Lankan authorities are exhuming the bodies of 15 aid workers who were massacred in the northeast of the country in August to try to establish who killed them, their French employer said.
The 15 were among 17 mainly Tamils who worked for Paris-based voluntary group Action Contre la Faim (ACF) and were found killed execution-style in their office compound in Muttur town after a battle in the area between the army and Tamil Tiger rebels.
An ACF statement said on Saturday: "The bodies should be transferred to Colombo the same day ... Australian experts are expected in Colombo next week to be present at the post mortem, principally as advisers and observers."
Nordic monitors of the tattered truce between the Sri Lankan army and Tamil Tiger rebels have formally accused government soldiers of being behind the Muttur killings.
The government has said that an earlier autopsy was inconclusive, and denies it was involved in the killings. Officials have accused the monitors of being biased in favour of the rebels. The inquest began in Muttur, but has since been transferred twice.
More than 65,000 people have been killed since 1983 when the rebels began fighting for an independent Tamil homeland.