Indonesia says it has won a two-year court battle that confirms the legality of the government's seizure of a Thai vessel linked to human trafficking and illegal fishing in Indonesian waters.

Minister of Fisheries and Maritime Affairs Susi Pudjiastuti said the "monumental" ruling from a court in Aceh province shows that governments can win in the fight against cross-border crime.

Pudjiastuti said in a statement this week that the ministry plans to make the refrigerated cargo ship Silver Sea 2 part of a museum to teach the public about illegal fishing.

The ship was seized by Indonesia's navy in August 2015 amid a crackdown on illegal fishing and after an Associated Press investigation showed its links to human trafficking in the fishing industry.

Several months before its capture, the ship and Thai fishing trawlers had abruptly left an island in remote eastern Indonesia, where the Thai fishing industry held trafficked crew members captive, to escape a government crackdown on illegal fishing.