The defence ministry said in a statement that naval craft called for air support after the unnamed vessel opened fire on patrol craft which ordered it to head to the northeastern naval port of Trincomalee.
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"When ordered by navy patrol craft to sail towards Trincomalee for checking, the vessel opened fire," the statement said, adding that fighter jets were called in to attack the ship.
The vessel was "suspected to be one ferrying arms and ammunition for the LTTE (Liberation Tigers of Tamil Eelam)," the ministry said.
There was no immediate reaction from the guerrillas to the military claim.
Analysts say the LTTE gets arms from manufacturers in China, Cambodia, Burma and states that were part of the former Soviet Union.
They say the arms are transferred at sea from large merchant ships, some owned by companies with links to the rebels, to small craft.
Earlier in the day, the guerrillas carried out artillery and mortar attacks against two military bases in the island's east and troop