Three activists who boarded a Japanese whaling ship on the high seas were Friday successfully transferred to an Australian customs vessel after Tokyo agreed to release them without charge.

The men from the Forest Rescue Australia environmental group boarded the Shonan Maru No.2, escorting Japanese whalers on an Antarctic hunt, off Australia's west coast on Saturday.

There were fears they would be taken to Japan and tried for trespassing but after a flurry of diplomatic activity, Tokyo on Tuesday decided to release them and an Australian ship diverted to pick them up en route to Antarctica.

Attorney-General Nicola Roxon said the men were transferred onto the ACV Ocean Protector using tenders without incident and appeared to be in good health.

She condemned Japanese whaling but warned protestors that similar action in the future could result in charges in Japan.

"We support peaceful protest, but dangerous action on the high seas is quite different. We strongly encourage both sides of this dispute to respect the law and act calmly," she said.

"Protestors must be aware that, in the future, such action may lead to charges in another country and possible conviction.

"The Australian government thanks Japan for its cooperation in the return of the Australian citizens," she added.

Forest Rescue said it boarded the vessel to try to prevent the Shonan Maru from tailing the Steve Irwin, a ship from anti-whaling group Sea Shepherd, back to the Southern Ocean where Japan annually hunts for whales.

The Steve Irwin returned to Australia last week because another Sea Shepherd ship, the Brigitte Bardot, was damaged in high seas and needed escorting home, setting back the group's annual harassment of the whalers.

It has since left to rejoin fellow Sea Shepherd ship, the Bob Barker, in pursuit of the Japanese fleet.

Commercial whaling is banned under an international treaty but Japan has since 1987 used a loophole to carry out "lethal research" on the creatures in the name of science.