Brigadier Prasad Samarasinghe said a dawn raid by Israeli-built Kfir jets "completely destroyed" a Liberation Tigers of Tamil Eelam (LTTE) base at Wilawattai in the rebel-held Mullaitivu district.
He said the base belonged to the Sea Tigers, the naval arm of the rebels.
There was no immediate comment from the rebels, whose territory in the north and east has been targeted by successive raids since Tuesday.
The LTTE's military spokesperson, Rasiah Ilanthirayan, however, accused government forces of killing two state employees and injuring three others in a fragmentation mine blast inside Tiger territory in Wanni district.
He blamed the Sri Lankan army's deep penetration units for triggering the explosion next to a jeep which transported the officials.
The LTTE wants a separate homeland for minority Tamils in the northern and eastern regions of the Sinhalese majority country.
The conflict has claimed more than 60,000 lives since 1972.