Officials said the base had earlier detected two suspicious aircraft hovering over the area and had gone on alert before the attack.
Residents nearby reported hearing loud explosions and gunfire throughout the morning, saying they saw repeated anti-aircraft fire coming from the base.
Four Sri Lankan air force personnel were killed when a helicopter gunship crash-landed several kilometres from the air base, an air force spokesman said.
The helicopter had been sent out to search the area after the attack on the air base.
The crash was due to technical reasons and not gunfire from LTTE fighters, the official said.
Details of casualties or damage were not immediately known, a military spokesman said.
Nanayakkara said the attack began early on Monday morning when a small group of separatist fighters infiltrated the air base from the ground and an air attack followed.
He said the fighting lasted for about two hours, with air force teams scouting the surrounding area looking for the attackers.
The Tigers are believed to have a small fleet of Czech-made Zlin Z-143 single-engine light aircraft, thought to have been smuggled in pieces by boat into northern Sri Lanka and can be flown from tiny makeshift airstrips in the jungle.
This is the first air strike since March, when Tamil Tigers launched their first ever air assault by bombing an air force base near Colombo.
Several other attacks included striking a fuel refinery and storage site.
Violence has escalated in recent months as troops and separatist fighters faced each other on the border separating the government-controlled area from the Tigers' home base.
Last week the Tigers infiltrated a wildlife park far south of their area and attacked a military camp there, killing seven soldiers.
The Tigers have been fighting for a separate homeland for minority Tamils in the island's north and east.
Tens of thousands have died since the separatist campaign was launched in 1972.