The trial of a New Zealand man arrested by the Japanese starts later this week and Prime Minister John Key said there was not much the Government could do if he faced jail time.

In February Peter Bethune, 42, boarded the Shonan Maru 2, hoping to make a citizen's arrest of its captain for allegedly ramming and sinking his ship.

Anti-whaling vessel Ady Gil sank after being sliced in two when it collided with the Shonan Maru 2 in the Southern Ocean on January 6 while it was harassing the Japanese whaling fleet.

Mr Bethune was arrested when the Shonan Maru 2 docked in Japan and is now in custody pending a trial on charges of trespass, causing injury, vandalism, carrying a knife and obstructing commercial activities.

His trial was scheduled to start on Thursday.

Mr Key said the Government was giving him all the consulate support it could.

"We can't necessarily stop (Mr Bethune serving jail time) in the same way that... these six Taiwanese people that have [allegedly] come in with $6 million worth of P, they are going to be convicted in the New Zealand courts, if they're found guilty they'll do a jail term here," he told TVNZ's Breakfast.

New Zealand's ambassador in Japan last saw Mr Bethune on Wednesday, Mr Key said.

The trial was expected to run three days and a verdict was due mid-June.

If convicted, Mr Bethune could receive up to 15 years in jail.