The Thai-owned Silver Sea 2 was located late yesterday and escorted about 80 miles (130 kilometres) to a naval base in Sabang on the Indonesian archipelago's northwestern tip, said Col Sujatmiko, the local naval chief.
The AP used a satellite beacon signal to trace its path from Papua New Guinea waters, where it was also being sought, into neighbouring Indonesia. The navy then spent a week trying to catch it. The ship was close to leaving Indonesian waters by the time it was finally seized.
The Silver Sea 2 is the same 2,285-ton vessel captured in a high-resolution satellite photo last month in Papua New Guinea showing its hold open and two fishing trawlers tethered to each side, loading fish.
The smaller wooden vessels were identified by analysts as the ones that fled the remote Indonesian island village of Benjina earlier this year, crewed by enslaved men from poor Southeast Asian countries who are routinely beaten and forced to work nearly nonstop with little or no pay.
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The businesses have all said they strongly condemn labor abuse and vowed to take steps to prevent it.
Pudjiastuti 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.
"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 said. He added that all of the ships' crews are Thai nationals and certified by the International Maritime Organisation.
The Indonesian navy has so far declined to comment on the crew found aboard the captured vessel.