Bethune, 45, had said he wanted to make a citizen's arrest of the ship's Japanese captain and hand over a $3m bill for the destruction of a protest ship that sank after an earlier confrontation with the Japanese whaling vessel.
Prosecutors say Bethune threw glass bottles with acid that exploded on the Japanese ship, injuring a crew member and obstructing the whaling mission.
"I admit that I boarded the Shonan Maru 2 but I believe that I have good reason to do so," he said during the proceedings.
"I admit that I fired the butyric acid, but there were additional circumstances that we will discuss in court."
Bethune was handcuffed and had a rope tied around his waste as he was ushered into the courtroom.
Protests and confrontations
Outside the court, a group of about 30 pro-whaling activists staged a protest.
|Protesters gathered outside the Tokyo court to criticise anti-whaling activists [Reuters]
Confrontations between the Sea Shepherd's boats and Japanese vessels have at times turned violent, forcing Japan's Antarctic whaling mission in recent years to return home with only half its catch quota of some 900 whales.
Japan joins Norway and Iceland in hunting whales under various exceptions to a 1986 moratorium by the International Whaling Commission (IWC).
Opponents say Japan's research whaling programme is a cover for commercial hunts and have singled it out for strong protests.
Japan's programme involves large-scale expeditions to the Antarctic, while other whaling countries mostly stay along their coasts.
Excess meat is sold in Japan for consumption, available through limited outlets such as special whale restaurants and public school lunch programmes.
The IWC, in a bid to resolve a deep divide between pro-whaling nations and their opponents, last month issued a proposal that would in effect allow the whaling countries to resume commercial hunts, though under strict quotas set by the commission.
Japan accuses conservationists of endangering the lives of whalers and is also seeking to arrest Sea Shepherd leader Paul Watson over his role in the Antarctic confrontation.