D K P Dassanayake, the navy spokesman, said rebels attacked a base in the town of Muttur on Tuesday "and we retaliated successfully."
He said the navy suffered no casualties. The rebels, who have their own well-armed army and navy, could not be immediately reached for comment.
There were no immediate further details on the attack, which came hours after the military accused the Tamil Tiger rebels of shooting at an ancient Buddhist shrine on Monday to provoke a backlash by the country's Buddhist majority.
A statement from the government's Media Centre for National Security said a group of rebels opened fire on Monday with small arms from three sides on the Somawathi shrine, about 170km northeast of Colombo.
Security forces guarding the shrine, believed to be about 2,000 years old, fired back, forcing the rebels to retreat, the statement said.
The attack was an attempt to "arouse the sentiments of the Sinhalese Buddhists against the innocent Tamils to cause Sinhalese-Tamil strife," the government statement said.
K P S Wickremesinghe, a local police officer, said there were no reported injuries and the shrine was not damaged.