The defence ministry said on Sunday that a suspected Tamil Tiger suicide bomber detonated explosives and destroyed a gun-running trawler off the island's northwest coast late on Saturday when challenged by the navy.
"As a naval fast-attack craft reached this trawler suspected to be carrying a stock of explosives, arms and ammunition, a 'Sea Tiger' suddenly blew himself up causing a huge explosion," the ministry said in a statement.
The blast completely destroyed the Liberation Tigers of Tamil Eelam (LTTE) trawler and four Sea Tigers on board were killed while a navy sailor was injured, the ministry said.
It said the Norwegian-led Sri Lanka Monitoring Mission (SLMM) was informed of the incident, which came after both sides had agreed to start two days of talks from 22 February on saving their troubled truce, which has been in place since February 2002.
There was no immediate reaction from the Tigers, but the pro-rebel Tamilnet.com website said the trawler exploded after it was intercepted by the navy.
The latest incident at sea came as Sri Lanka's warring parties prepared to go to Geneva for face-to-face talks.