Australian Greens leader Bob Brown is angry Australian Federal Police are searching the anti-whaling ship the Steve Irwin in Hobart, saying the federal government has caved in to pressure from the Japanese.

The Sea Shepherd has ended its summer campaign against the Japanese whaling fleet and docked at Princes Wharf at 8.30am (local time) on Saturday.

The boat was greeted by a crowd of well wishers but federal police officers were also there - armed with a search warrant.

Greens leader Bob Brown said federal police were executing the warrant at the request of Japanese authorities in Tokyo.

"This is outrageous that Australian police are at the disposal of the Japanese whale killers," Senator Brown told the welcoming crowd.

"Tokyo has taken over Australia's Antarctic seas and whales and now it controls events in Hobart."

Senator Brown said the search warrant used to raid the vessel alleges breaches of Australian law, not Japanese law.

"The search warrant invokes a lot of potential claims of infringement of laws, obscure or otherwise, under Australian law.

"The spineless Rudd government has laid charges, including throwing of rancid butter.

"I am not the only person around the world that is very angry at what's happening here.

"Shouldn't the Australian police be waiting on the docks in Tokyo for the real criminals here?"

A spokeswoman for Senator Brown said video material onboard the ship was being investigated by the police.

The 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 that vessel.

An AFP spokesman said a number of officers boarded the Steve Irwin 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 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.