Two of the rebel boats were destroyed in the air strike at 6.20 am. One sank immediately while the other caught fire.
The boats were one kilometer north of Mullaithivu lagoon in the sea.
Air force officials said there were large concentrations of rebel vehicles on the beach.
An army battle group is approaching the Tiger Mullaithivu base from the south.
Military officials said the rebels were trying to smuggle heavy weapons to help ward off the army attack.