AFP board anti-whaling ship

Steve Irwin captain Paul Watson

THE Australian Federal Police have boarded the anti-whaling ship the Steve Irwin in Hobart, following a request from Japan.

The Sea Shepherd's Steve Irwin docked at Princes Wharf at 8.30am (AEDT) on Saturday, after an engine problem forced them to end this season's campaign against Japanese whalers in the Southern Ocean.

Australian Greens Leader Bob Brown said federal police are executing a search warrant at the request of Japanese authorities in Tokyo.

"At least five federal police officers have boarded," Senator Brown said in a statement.

"This is outrageous that Australian police are at the disposal of the Japanese whale killers."

A spokeswoman for Senator Brown said the search warrant is vague and it is not clear what federal police are searching for, but video material is being investigated.

Captain of the ship Paul Watson has been released from the boat, but his colleagues don't have permission to leave at this stage.

The Sea Shepherd's second anti-whaling boat the Bob Barker is also due to dock in Hobart at 2.30pm on Saturday.

Federal Police are yet to confirm if they will search the vessel.

An AFP spokesman on Saturday said a number of officers boarded the ship soon after it docked in Hobart on Saturday morning.

"As a result of a formal referral from Japanese authorities the AFP can confirm it conducted a search warrant on board the Steve Irwin this morning," the spokesman said.

The search was still underway at midday (AEDT).

The spokesman declined to say if anything had been seized from on board the boat or if any of its crew would be interviewed by police.

The Sea Shepherd activist boat has ended its summer clashing with the Japanese whaling fleet in the Southern Ocean.

Those clashes have included a collision between another activist boat, the Ady Gil, and a Japanese whaling ship, that led to Ady Gil being damaged and abandoned at sea.

The Ady Gil's captain Peter Bethune was later detained by the Japanese on board their boat Shonan Maru 2 after he boarded that vessel without invitation.