A New Zealand anti-whaling activist held on a Japanese harpoon ship he boarded in Antarctic waters last month was expected to arrive in Tokyo Bay on Friday and face arrest.

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Peter Bethune is a member of the militant Sea Shepherd Conservation Society and was the captain of a high-tech powerboat that was sliced in two in a collision with the whaling ship Shonan Maru II in January.

He climbed aboard the Japanese ship before dawn on February 15 from a jet ski with the stated intent of making a citizen’s arrest of its captain Hiroyuki Komiya for what he said was the attempted murder of his six crew.

Bethune also presented the Japanese whalers with a $US3 million($A3.28 million) bill for the his boat, the futuristic carbon-and-kevlar trimaran Ady Gil, which sank in the icy waters a day after the collision on January 6.

Instead, the Japanese whalers took Bethune into custody and sailed for Japan. They reported he was in good health and being treated well, unrestrained but under watch in a private cabin with three meals a day.

The Sea Shepherds, who have called Bethune the first New Zealander taken as a “prisoner of war” to Japan since World War II, said on their website that they were preparing legal representation for the skipper.

In a phone call with New Zealand officials, Bethune has “indicated he was happy to remain on board the Shonan Maru II and return to Japan with the vessel”, Foreign Minister Murray McCully said last month.

Japan’s Coast Guard plans to arrest and question the New Zealander on suspicion of trespassing on a vessel when the ship returns to port, Japanese newspapers and news agencies have reported.

If indicted, tried and convicted, Bethune could face up to three years in prison or a maximum fine of Y100,000 ($A1,206.49).

Commercial whaling has been banned worldwide since 1986, but Japan justifies its annual hunts as “lethal scientific research”, while not hiding the fact that the meat is later sold in shops and restaurants.

Australia has threatened to take international legal action against Japan if it does not commit to end whaling this year.

Sea Shepherd declared an end to this season’s pursuit of Japanese harpoon ships in Antarctic waters on February 27, saying it had been their most successful campaign so far.

The harassment by the group, which has hurled rancid-butter stink bombs and aimed water cannon at the whalers, has infuriated Japan.

Australian police searched two Sea Shepherd ships at the request of Japanese authorities last Saturday, seizing log books and videos.

Bethune’s case is not the first time Sea Shepherd activists have boarded Japanese whaling ships. In 2008 a Briton and an Australian climbed aboard a Japanese harpoon vessel to deliver a protest letter. After two days the Japanese side handed them back to an Australian customs boat.

If Bethune faces trial in Japan, it would be the second court case there centred on whaling. Proceedings are under way against two Japanese Greenpeace activists in the northern city of Aomori.

The so-called “Tokyo Two” face up to 10 years in prison for theft and trespassing after they took a box of salted whale meat, which they said was proof of embezzlement in Japan’s state-funded annual whaling expeditions.