Sea Shepherd activists claim they have conducted a citizen's arrest in the Southern Ocean on a Nigerian-flagged fishing boat known for poaching Patagonian toothfish and other rare species.

Crew members from the environmental activist group's ship, the Bob Barker, said they intercepted the Thunder in a fishing area regulated by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) without a permit to fish.

The Thunder is on a list of boats deemed to have engaged in illegal, unreported or unregulated fishing activities by CCAMLR.

Bob Barker captain Peter Hammarstedt said he made radio contact with the captain of the Thunder on Wednesday afternoon, between Heard Island and Davis Station, just outside Australia's territorial waters.

"They then told me by radio they were not fishing, they were just passing through these waters," he said.

"It's a vessel that Australia and New Zealand law enforcement authorities are looking for, and we know that they are making millions of dollars a year by fishing Antarctic and Patagonian toothfish illegally.

"This vessel is most certainly not allowed in the region that we found them in.

"They're blacklisted by CCAMLR, which is the regulatory authority which governs fisheries down in the Southern Ocean.

"It's wanted by Interpol and we have done a citizen's arrest of this vessel."

Mr Hammarstedt said he had ordered the boat to report to Fremantle and would continue trailing it.

"We're now calling on Australian authorities to take over this arrest from us," he said.

The Greens are angry Patagonian toothfish poachers returned to the Southern Ocean after their ship was impounded in May.

Tasmanian Greens Senator Peter Whish-Wilson said the Thunder was impounded by the Federal Government.

"We know nothing about the level of fines that were imposed on the boat or what actually happened to the crew but now we know to our surprise and disgust that this vessel is back down in the Southern Ocean fishing illegally," he said.

The senator said he wanted the Australian Government to do more.

"The Government promised they would send two 40-day patrols down to the Southern Ocean this summer to send the poachers on their way and to save life at sea, where is that vessel?" he said.

"Why hasn't it been sent yet and why is it up to the Sea Shepherd to actually go down and police our fisheries which is the Government's job."

In a statement, Immigration and Border Protection Minister Scott Morrison said Australia would deal with any unlawful activities in the Southern Ocean in accordance with domestic and international laws.