Greens Senator Bob Brown says it is horrendous that a New Zealand anti-whaling activist is facing the prospect of a lengthy jail term in Japan.

Sea Shepherd activist Peter Bethune jumped on board a Japanese whaling ship in Antarctic waters about a month after his ship was destroyed in a clash with the whalers.

A series of recommendations by the Japanese coastguard, obtained by the ABC, urges prosecutors to charge Mr Bethune with damaging property, obstructing the business of the whaling fleet, carrying a knife and causing bodily injury.

The charge of causing bodily injury could incur a maximum prison sentence of 15 years.

Senator Brown says it seems to have been forgotten that the Japanese whalers ran down Mr Bethune's ship, the Ady Gil, endangering the lives of the six people on board.

He says Mr Bethune and his crew were almost killed when the Shonan Maru II rammed their ship.

"It's time that Canberra and Wellington took up that matter with the Japanese government and with great vigour prosecute the Shonan Maru's captain and his crew, who took part in that illegal act in destroying the Ady Gil," he said.

Senator Brown is urging Australia take retaliatory legal action.

"The Australian Federal Police and the New Zealand police are investigating that sinking of the Ady Gil and the Australian and New Zealand governments should be pursuing with great vigour that investigation and charges against the whaling fleet," he said.

The Japanese coastguard alleges Mr Bethune used a knife to cut through a net and board the whaling ship.

It also claims he threw containers of butyric acid, or rancid butter, against the side of the ship, splattering a crewman and injuring his face.

Mr Bethune has defended his actions, claiming his intent was to make a citizen's arrest of captain Hiroyuki Komiya for what he says was the attempted murder of his six crew.

After boarding the whaling ship, Mr Bethune also presented the Japanese whalers with a $US3 million ($3.27 million) bill for the futuristic carbon-and-kevlar trimaran, which sank in the icy waters a day after the collision on January 6.