Japan and Australia have avoided a diplomatic row following the decision to release without charge three environmental activists who clambered aboard a Japanese whaling ship off the west coast of Australia at the weekend.

The three Australian citizens boarded the Shonan Maru 2, which is providing security to Japan's whaling fleet, to demand an end to this year's hunt in the Antarctic.

Concern that the men - Geoffrey Tuxworth, Simon Peterffy and Glen Pendlebury - would be held on board the ship and taken back to Tokyo to face possible criminal charges faded after Japan agreed to release them without charge.

Australia's prime minister, Julia Gillard, thanked the Japanese government for its co-operation, but warned activists against attempting another boarding as they attempt to disrupt the hunt.

Gillard said in a statement that the men's actions had been "unacceptable and will ultimately be costly to the Australian taxpayer".

She added: "No one should assume that because an agreement has been reached with the Japanese government in this instance that individuals will not be charged and convicted in the future.

Kyodo quoted unnamed sources as saying Japan had decided not to charge the activists because no crew members had been harmed during the boarding.

Gillard said Australia would continue its legal campaign to end the hunts. Last year, Australia filed a complaint against Japan at the world court in the Hague. A decision is expected in 2013 at the earliest.

The detained men, who belong to a group called Forest Rescue, will have to remain on board the Shonan Maru 2 for several days while an Australian customs vessel sails out to collect them.

Japan is permitted to catch a limited number of whales every year under a clause in the 1986 ban on commercial whaling. Last year the fleet returned to port with just one-fifth of its quota after a series of confrontations with Sea Shepherd.

The group's founder, Paul Watson, welcomed Japan's decision but repeated calls for the Australian government to honour an election pledge to end the whale hunt.

"We are down there to protect the whales, we are not down there to make everybody happy," he said in a radio interview from the Steve Irwin, a Sea Shepherd boat being shadowed by the Shonan Maru 2 as it attempts to locate the whaling fleet's mother ship.

"If the Australian government would do their job and fulfil their election promises, these things wouldn't happen."

Watson said on Monday the boarding had taken place while the Japanese vessel was in Australian territorial waters, a claim denied by authorities in Tokyo and Canberra.

In 2010, a Tokyo court gave Sea Shepherd member Pete Bethune a suspended sentence after he boarded the Shonan Maru 2 to protest against a collision in which the group's hi-tech speedboat sank.