The captain of an Antarctic anti-whaling boat has performed a daring night-time boarding of the Japanese whaler that sank his multimillion-dollar vessel.

Pete Bethune, skipper of the stricken Ady Gil, early yesterday boarded the Shonan Maru 2 from a jet ski in order to make what fellow protesters described as a citizen's arrest of its captain.

Mr Bethune has filed a complaint with New Zealand police, alleging the captain of the Shonan Maru 2 rammed and sank his ship and attempted to murder the crew during the January 6 incident.

Not content with trying to arrest the Japanese captain, Mr Bethune was also to present a $3 million bill to the whalers for the cost of replacing the Ady Gil.

"Pete presented the skipper with a demand that he turn himself in to a New Zealand or Australian port in order to answer to charges of destroying the Ady Gil and the attempted murder of six Sea Shepherd [Society] crew members," said Sea Shepherd captain Paul Watson.

"Of course we know they're not going to do that, but we have to press the case. They destroyed our ship without any repercussions."

Mr Bethune was detained aboard the Shonan Maru 2, and it is possible he will be forced to stay with the ship until its return to Japan.