Peter Bethune of the militant Sea Shepherd Conservation Society was engaged in months of high-seas clashes with the Japanese whaling fleet but has been in custody since mid-February when he boarded the Shonan Maru II.

About 20 angry nationalist protesters with Rising Sun flags, watched over by riot police, lined the pier and shouted through megaphones: "Step forward Pete Bethune! Apologise to the Japanese people! We will tear you apart!"

The harpoon ship docked alongside a vessel of the Japan Coast Guard, whose officers served him with an arrest warrant for trespass on a ship, a charge that can carry up to three years' jail.

Bethune was in good shape, did not resist arrest, and was due to face questioning and meet New Zealand embassy officials later in the day, Takeo Murui, the Tokyo Coast Guard office chief, told a news conference.

It was the latest chapter in a long-running battle between environmentalists and Japanese whalers, who hunt the ocean giants in the name of scientific research, a loophole to a 1986 international moratorium on whaling.

Japan maintains that whaling has been part of the island-nation's culture for centuries, and it does not hide the fact that whale meat from its annual expeditions ends up in shops and restaurants.

As TV helicopters buzzed overhead, the protesters -- watched by riot police and plain-clothed officers with video cameras -- also expressed their fury with Australia, which has threatened legal action over Japan's whale hunts.

Fisheries Minister Hirotaka Akamatsu said Japan would maintain a "resolute stance" but said he did not see a diplomatic row brewing.

Foreign Minister Katsuya Okada said: "We have repeatedly showed our concern that the Sea Shepherds' obstruction of our research whaling is very vicious. We have also been discussing the issue with the Australian government.

On Bethune's case, Okada told a press conference: "I think the case will go forward in an orderly way in line with judicial procedures. We had better not comment on whether he will be prosecuted."

Bethune, 44, was the captain of the Sea Shepherds' high-tech powerboat that was sliced in two in a collision with the Shonan Maru II in January.

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

Bethune also presented the Japanese whalers with a three-million-dollar bill for 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 they were preparing legal representation for the skipper.

The group declared an end to this season's three-month pursuit of Japanese harpoon ships in Antarctic waters on February 27, saying it had been the most successful campaign yet because it had stopped all whaling on 33 days.

If Bethune faces trial, it would be the second court case in Japan centred on whaling.

Proceedings are ongoing against two Japanese Greenpeace activists now in the dock in the northern city of Aomori, who face up to 10 years in prison for theft and trespassing.

The so-called "Tokyo Two" took a box of salted whale meat from a delivery depot, which they said was proof of embezzlement in Japan's state-funded annual whaling expeditions. They then handed the box of meat to prosecutors.

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