A Sri Lankan air force official said the base was located in the Pulopalai area in Muhamalai. Reports of casualties weren't available.
The raids occurred as the rebel group asked priests at a historic church in Mannar district in the northwest to evacuate the facility, the Press Trust of India reported. The area is regarded a rebel stronghold.
PTI, quoting sources, said several civilians to fled the area after the Tamil rebel group allegedly placed heavy mortar and artillery near the church.
Violence on the Indian Ocean island has risen sharply as both the Sri Lankan military and rebels have stepped attacks with the collapse of a cease-fire brokered by Norway in 2002.
The Tigers have been fighting since 1983 for an independent homeland for the Tamil-speaking minority in the predominantly Buddhist nation.