Anti-whaling activist Pete Bethune, imprisoned in Japan, believes he will be found guilty and fears a lengthy jail sentence.

New Zealander Bethune, 42, is awaiting a trial on charges of trespass, causing injury, vandalism, carrying a knife and obstructing commercial activities.

He was arrested in February when he boarded Japanese whaling vessel Shonan Maru 2 in the Southern Ocean, hoping to make a citizen's arrest of its captain for allegedly ramming and sinking his ship.

The Ady Gil sank after colliding with the Shonan Maru 2 the previous month while it was harassing the whaling fleet.

Bethune, who faces up to 15 years in jail, believes there is a 95 per cent chance he will be convicted at his trial, which starts on Thursday, and worries he will be sentenced to a long prison term, the Sunday Star-Times reported.

Speaking from the Tokyo Detention Centre, he said authorities have treated him like a terrorist or a "psychopathic killer."

Bethune had been taken back to the Shonan Maru to re-enact the boarding, accompanied by a security detail of more than 100 people, he said.

"I had a hood over me, like I'm a psychopathic killer. It was bizarre."

Bethune holds little hope of a suspended sentence and deportation to New Zealand.

However, he did have a message for Prime Minister John Key in the lead-up to an International Whaling Commission meeting next month to consider a proposal to allow limited commercial whaling.

"He'll betray us if he signs that and he'll go down in history as the man who brought whaling back," he said.

Meanwhile, his wife Sharyn revealed financial and personal pressures of her husband's long absences have caused the couple to separate.