The Silver Sea 2 was captured after the Associated Press used a satellite beacon signal to trace its path from Papua New Guinea waters, where it was also being sought, into neighboring Indonesia. The navy then spent a week trying to catch it.
"I'm so overwhelmed with happiness," said Fisheries Minister Susi Pudjiastuti, adding it was difficult to find because the boat's signal had a delay. "It was almost impossible, but we did it."
The Silver Sea 2 was photographed last month in Papua New Guinea with two fishing trawlers. Earlier this year, those trawlers fled the remote Indonesian island village of Benjina, where enslaved men from poor Southeast Asian countries are forced to work.
An investigation by the Associated Press revealed that the fish the slaves caught reached major US food sellers, such as Wal-Mart, Sysco and Kroger, and American pet food companies, including Fancy Feast, Meow Mix and Iams.
Those companies have all said they strongly condemn labor abuse and vowed to take steps to prevent it.
Indonesia freed hundreds of men earlier this year after the AP exposed they were trapped – including some locked in a cage – on Benjina. But 34 boats loaded with slaves escaped before authorities arrived. They remain missing.
Seven arrests have been made in Indonesia and two in Thailand related to the case, according to the AP.
On Thursday, an official at Silver Sea Reefer Co., which owns the Thai cargo ship, denied that the Silver Sea 2 had been seized, and said its business was not connected to human trafficking.
"We have received numerous calls from Thai agencies… asking about this and basically we said we have never done anything like it," company manager Venus Pornpasert told the AP. He added that all of the ships' crews are Thai nationals who are certified to work.
However, the AP spoke with hundreds of enslaved workers from Myanmar who said they had been trafficked in Thailand and brought to fish in Indonesia aboard the Silver Sea 2.
Indonesian authorities will question the captain of the Silver Sea 2 and launch an investigation into suspected human trafficking and the transportation of illegally caught fish.
Two weeks ago, authorities in Papua New Guinea seized another Thai-owned cargo ship. Two trafficked Burmese and six Cambodians were found on board, the AP reported.