The defence ministry said Tiger aircraft had dropped two bombs and fled the town.
Residents reported anti-aircraft fire, in a town which has had its power supply disrupted by a freak cyclone.
The Tiger aircraft fly low to avoid radar detection and usually manage to slip way from interceptors that are scrambled to meet them.
Tamil Tiger guerrillas previously used light aircraft to raid Sri Lanka's capital Colombo, but the converted light aircraft can only carry a small bomb load.
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Trincomalee is home to an important naval base.
Tamil Tiger have been waging a separatist war over three decades, but the group has lost territory to government forces over the last year.
The military says they are now 12 kilometres away from the Tiger stronghold of Kilinochchi which is considered the 'capital' of the areas controlled by the guerrillas.