The federal government has distanced itself from an Australian Federal Police (AFP) raid on the anti-whaling ship Steve Irwin made at the request of the Japanese.
Australian Greens leader Bob Brown is demanding the federal government explain why the AFP raided the Sea Shepherd vessel on Friday evening in Hobart.
But a spokeswoman for Home Affairs Minister Bob Debus said the matter was in the hands of the AFP.
"All we can say is that it's an operational matter and it would be inappropriate to comment," the spokeswoman said.
"It's like any police investigation."
After violent clashes with Japanese whalers in the Southern Ocean, the Steve Irwin was met by the AFP when it docked in Hobart early on Friday evening (AEDT) and officers confiscated the ship's log book and video footage.
The footage, taken by wildlife documentary group Animal Planet, depicted some of the most dramatic whale-killing scenes ever seen, crew on the Sea Shepherd Conservation Society ship said.
The police, who had search warrants, kept the crew on board as they searched cabins.
Senator Brown has written to Prime Minister Kevin Rudd calling for an immediate explanation as to how the raid could be in the nation's interest.
"On the face of it, this is outrageous behaviour by the Australian government to secure favour from the Japanese authorities," he said.
An AFP spokeswoman confirmed an investigation was launched at the request of the Japanese authorities, who this year complained after activists threw bottles of rancid butter at the whalers and tried to board a ship.
"I can confirm that a raid took place," an AFP spokeswoman said.
"An investigation was launched at the request of the Japanese authorities."
Senator Brown said the raid would outrage many Australians.
"The Australian Federal Police can expect detailed questioning from the Greens at Senate Estimates this coming week," he said.
Senator Brown said he had been told by Steve Irwin captain Paul Watson that the ship was delayed coming into the port in Hobart so that the AFP had time to make their raid.
"I'm also told that the Japanese used absolutely outrageous tactics, like sound wave attacks on people in helicopters, which could have brought down those helicopters from the Sea Shepherd."
Steve Irwin captain Paul Watson said the Steve Irwin had never been searched before but he would welcome any facing a court.
"My position is that if they want to put me on trial for anything connected with this, then I am happy to do it," Capt Watson told the Hobart Mercury.
"We are not there protesting, we are down there to stop a blatantly criminal activity, to stop whaling in a whale sanctuary.
"These actions have to go to court somewhere, so let's start it here."
Japan slaughters whales using a loophole in an international moratorium on commercial whaling that allows "lethal research" on the mammals.