The anti-whaling group Sea Shepherd said three Australian activists were being held as "prisoners" by the Japanese harpoon fleet Sunday after sneaking aboard one of their vessels overnight to protest.

Sea Shepherd said it had helped the three men from the Forest Rescue Australia environmental group to board the Shonan Maru No.2 16 miles (26 kilometres) off Australia's west coast.

"The boats approached the Shonan Maru under the cover of darkness and the three negotiated their way past the razor wire and spikes and over the rails to successfully board the Japanese whaling vessel," Sea Shepherd said of the Forest Rescue trio.

They were now "being held as prisoners on board the Japanese vessel the Shonan Maru No.2" which had been tailing the Sea Shepherd ship the Steve Irwin and had "armed Japanese military personnel," Sea Shepherd claimed.

Japan's Fisheries Agency confirmed that three men who said they were Australian had boarded the Shonan Maru No.2 -- a surveillance craft -- and that there were coastguard officers on board the ship.

"Three men on a rubber boat quickly approached the Fisheries Agency's monitoring vessel and climbed to the ship," a fisheries official told AFP.

"Currently the Fisheries Agency is interviewing the men.

"This incident did not cause any injury to the (Japanese) crew (or) damage to the ship," he added.

Australian Attorney-General Nicola Roxon said Canberra was in contact with Tokyo to determine the Shonan Maru's exact location but no application had been made to bring the protesters ashore and they could end up in Japan.

"It appears that the laws that will cover (their) detention, for want of a better word, is the Japanese law," said Roxon, adding that the men's safety was the government's "top priority".

"We know there is a risk protest action will be taken and know there is a risk it might get out of hand in either direction."

"We now need to do what we can through diplomatic channels to see if we can support them to make sure that they can be returned safely and promptly to Australia," she added.

It is not the first time an activist has boarded the Shonan Maru No.2 -- New Zealander Pete Bethune was arrested and taken back to Japan to be tried after sneaking onto the ship during the heated 2009-2010 campaign.

He was handed a two-year suspended sentence and spent five months in prison.

In a statement Forest Rescue said it wanted to prevent the Shonan Maru from following the Steve Irwin back to the Southern Ocean.

The Steve Irwin had to return to Australia last week because another Sea Shepherd ship, the Brigitte Bardot, was damaged in high seas and had to be escorted home for repairs, setting back the group's annual harassment of the whalers.

Forest Rescue said it was "making a stand to assist Sea Shepherd Conservation Society in their campaign to end illegal whale poaching in the Southern Ocean Whale Sanctuary."

"We are taking this action to remind the Australian government of their obligation to enforce existing laws pertaining to the prohibition of whaling ships in our waters," the group added.

"Forest Rescue are insulted and disappointed in our government for allowing the transit of whale poaching vessels in Australian waters."

The group has demanded that the Japanese return the protesters -- Simon Peterffy, 44, Geoffrey Tuxworth, 47 and Glen Pendlebury, 27 -- to shore and leave Australian waters.

Commercial whaling is banned under an international treaty but Japan has since 1987 used a loophole to carry out "lethal research" in the name of science -- a practice condemned by environmentalists and anti-whaling nations.

Australia has taken Japan to the International Court of Justice seeking an end to its annual hunts but one of the men who boarded the Shonan Maru, Peterffy, said not enough had been done.

"We are on board this ship because our government has failed to uphold its pre-election promise to end whaling in the Southern Ocean," he said, according to the Forest Rescue statement.