A New Zealand anti-whaling activist was arrested in Japan Friday after a harpoon ship he boarded in Antarctic waters last month docked in Tokyo, greeted by police and nationalist protesters.

Peter Bethune, of the militant Sea Shepherd Conservation Society (SSCS), 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.

It is 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 moratorium on whaling.