A government spokesman said one of the captured men identified himself as a Tamil Tiger and said the boat was carrying guns and mortar bombs.
Maldivian fishermen spotted the Tigers boat on Wednesday evening and gave chase after believing it was a fishing boat poaching in their waters, Mohamed Hussain Shareef, Maldives government spokesman, said.
When the boat's crew opened fire on the fishermen, they informed the Maldivian coast guard, which later sank it after a standoff, Shareef said.
The incident took place several hundred nautical miles off the south of the Maldives archipelago.
Sri Lanka's Navy has sunk several boats and trawlers in recent months suspected of trafficking weaponry for the Tigers across the Palk Strait that separates Sri Lanka and India.
The Tamil Tigers, fighting for an independent state in Sri Lanka for ethnic Tamils, were not immediately available for comment.