An Australian customs vessel was Tuesday steaming towards a Japanese whaling ship to pick up three activists held on board 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, about 16 miles (26 kilometres) off Australia's west coast on Saturday night.

There were fears the trio would be taken to Japan and tried for trespassing but after a flurry of diplomatic activity Australian Attorney General Nicola Roxon said Tokyo had decided to release the men.

"We are pleased that the Japanese government has made a decision that these three men won't be charged and will be released," she told reporters.

"But we can't be confident that will happen next time if people take action, take the law into their own hands."

Consular officials had been in contact with the men and they were well, she added.

An official from Japan's Fisheries Agency said the decision to release the men had been made by the Japanese government based on the facts of the case.

"They did not commit any violent acts after boarding the ship. In addition, it was not believed that they had been involved in previous acts of sabotage carried out by Sea Shepherd members in the past," the official said.

Prime Minister Julia Gillard thanked the Japanese government for their cooperation and said a ship had left port to meet up with the Shonan Maru.

"The Gillard government has dispatched the Ocean Protector, a customs vessel, to rendezvous with the Shonan Maru 2 and take the three Australians back to Australia," a spokesman said in a statement.

"It is anticipated that this will take some days, and be subject to weather conditions."

While the Gillard government is opposed to whaling, it stressed such "hazardous protest activity" undertaken by the three Forest Rescue demonstrators was not the way to end the practice.

"Activity of the nature undertaken by these three Australians is unacceptable and will ultimately be costly to the Australian taxpayer," the statement said.

"The best way to stop whaling once and for all is through our court action in the ICJ (International Court of Justice)."

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 anti-whaling campaign.

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

Forest Rescue said it boarded the vessel to try and 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.

The Steve Irwin left over the weekend to rejoin fellow Sea Shepherd ship, the Bob Barker, in pursuit of the Japanese whaling fleet, with the Shonan Maru on its tail.

Three whaling ships, led by the 720-tonne Yushin Maru, left the Japanese port of Shimonoseki on December 6 for the annual hunt, with security measures beefed up amid simmering international protests.

In previous years, a mother ship has joined the whalers later.

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.