Japan reportedly plans to arrest a New Zealand activist being held on a whaling ship which he secretly boarded, planning to make a citizen's arrest of its captain.

Peter Bethune, a member of the anti-whaling Sea Shepherd Conservation Society, has been in Japanese custody since he climbed aboard the vessel in Antarctic waters in mid-February to make a citizen's arrest over the sinking of his high-tech protest boat.

The Japan Coast Guard planned to arrest the New Zealander upon the ship's return to Tokyo, which was expected to be on Friday, Japan's Asahi Shimbun newspaper said, quoting anonymous investigation sources.

If convicted, Mr Bethune could face imprisonment of up to three years or a maximum fine of Y100,000 (about $1500).

Mr Bethune was the captain of the trimaran, Ady Gil, which was destroyed in a collision with the whaling vessel on January 6.

The activists declared an end to this season's pursuit of Japanese harpoon ships in Antarctic waters on February 27, saying it was their most successful campaign so far.

The group's anti-whaling vessels, the Steve Irwin and the Bob Barker, arrived in Hobart on Saturday, marking the end of their summer campaign.

But as the two ships docked in Hobart, the Australian Federal Police raided the vessels at the behest of Japanese authorities.

Sea Shepherd boss and the ship's captain Paul Watson was detained and his crew interviewed before they were released.

Mr Watson said there was a possibility the raids could lead to a court case.

"They've already seized log books, videos, photographs, charts, GPS recordings and copies of the computer hard drives," he told AAP.

"There's nothing I would love better than to have this whole thing blow up in an Australian court, let's clean all the laundry once and for all."

A federal police spokesman told AAP the ships were searched "as a result of a formal referral from Japanese authorities".

"... As inquiries are ongoing, it's inappropriate to comment any further at this stage," the spokesman said.

Mr Bethune's case is not the first time Sea Shepherd activists have boarded Japanese whaling ships. In January 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.

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.