Former Greens leader Bob Brown says fear of a diplomatic fallout is preventing Australia from standing up to Japan on whaling.

Dr Brown, who is now a member of the Sea Shepherd board, also stood behind Sea Shepherd skipper Paul Watson, who jumped bail in July in Germany while being detained over an incident off the coast of Costa Rica in 2002.

The former senator says he wants the Australian Government to seek an international court injunction to stop Japan's annual whale hunt in the Southern Ocean.

"They're worried. They want a free-trade agreement, they're worried that this is going to, in some way or other, annoy politicians in Tokyo," he said.

"There's a lot of Australians who are annoyed that the Australian Government, and indeed the Opposition when it was in government, haven't stood up to the Japanese. And it's time they did."

Dr Brown said he has nothing but praise for Watson.

Interpol has issued an arrest alert for Watson, who is wanted in Costa Rica over charges relating to a confrontation over shark finning.

Watson has since said he is back on board an activist vessel and ready to confront whalers.

"I've admired Paul Watson and Sea Shepherd for 30 years," Dr Brown said.

"They have done a fantastic job. It's been non-violent, they have never harmed anybody in that process."

The former senator also wants the Government to ensure the safety of the Sea Shepherd's four ships and crew.

"This time they (the Japanese) have armed coastguard people - this is men with guns on their ships coming into the demilitarised zone in Antarctica - while our Government and governments elsewhere sit on their hands and allow this international law-breaking," he said.

"It's Sea Shepherd that's upholding the law here."