"There is a probe underway to establish how the gunboat was hit," a defence official said.
"The initial report from the navy is that six Tigers on the trawler blasted themselves and the impact of that explosion sank the gunboat.
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The gunboat was on a mission to check gun running in the area, officials said.
The ministry said the sinking of the navy craft was a violation of a truce arranged by Sri Lanka's peace broker Norway and lodged a complaint with the Scandinavian ceasefire monitors.
"The suicide-style explosion carried out by the crew of the trawler causing damage to a naval vessel and claiming the lives of navy personnel is a violation of the ceasefire," the defence ministry said in a statement.
Eleven sailors were rescued by local fishermen.
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In January, suspected Tamil Tiger rebels blew up a simila