The air force targeted the boatyard in Iranaimadu, close to the rebels' de facto capital, Kilinochchi, the defense official said on condition of anonymity, citing government regulations.
He said pilots confirmed they hit the target, though he did not provide details.
Rebel spokesman Rasiah Ilanthirayan denied that their boatyard was hit but said bombs fell into a housing complex, wounding a civilian.
On Thursday, five separatist rebels were killed in three clashes reported across northern Sri Lanka , the official said.
Four rebels were killed and a soldier wounded in two clashes in Vavuniya district, south of Kilinochchi, he said. In another incident, soldiers pushed into rebel territory across a defense line in Nagarkovil in Jaffna peninsula, killing one rebel, the official said.
Ilanthirayan acknowledged clashes across front lines in the north, but denied that five rebels were killed.
It was not possible to independently verify the conflicting claims for either the airstrike or the clashes.
Fighting has escalated in recent months along lines that separate the government and rebel-controlled territories in the north. The Tamil Tigers have their own police, courts and administration in some parts of the north, which the government has vowed to dismantle.
The rebels have fought the government since 1983 to create a separate homeland for ethnic minority Tamils after a history of discrimination by the ethnic Sinhalese-controlled governments.
More than 70,000 people have been killed in the violence.
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