But he denied the charge of assault, in which prosecutors say a 24-year-old whaler suffered chemical splash burns to his face, during a February 11 confrontation when Sea Shepherd activists hurled the butyric acid stink bombs.
Japan hunts whales under a loophole in an international moratorium that allows killing of the ocean giants for what it calls "scientific research", although the meat is later sold openly in shops and restaurants.
"I think they wanted this case out of the way as soon as possible, considering the amount of worldwide attention it has received"
Sea Shepherd founder
The Sea Shepherd group has pursued and harassed Japanese whalers in Antarctic waters for years - most recently in the 2009-2010 season, a campaign which both sides say reduced the Japanese cull by several hundred whales.
In their annual clashes, the adversaries regularly trade icy jets from water cannon, while the environmentalists also hurl blood-red paint containers.
Bethune, a New Zealand national, was captain of the group's futuristic carbon-and-kevlar powerboat, the trimaran Ady Gil, which sank after a January 6 collision with the Japanese fleet's security ship the Shonan Maru II.
On February 15, Bethune boarded the Shonan Maru II from a jet ski before dawn, with the stated intent of making a citizen's arrest of its captain and presenting him with a $3 million bill for the Ady Gill.
Instead, he was detained and taken back to Japan, where he was formally arrested on March 12 and has been in detention since.
The Japanese coastguard has also filed a request with Interpol to place Sea Shepherd's Canadian founder Paul Watson on its international wanted list, on charges of instructing Bethune to interfere with Japanese whaling.
Watson told Al Jazeera on Wednesday that the verdict against Bethune showed the Japanese government's embarrassment over this issue.
"I think they wanted this case out of the way as soon as possible, considering the amount of worldwide attention it has received," he said.
|Despite claims of 'scientific research', whale meat is quite popular in Japan [EPA]
"Japan been extremely embarrassed by this, and a negative spotlight has been placed on its activities.
"The government usually did its whaling without much attention, but when NGOs like ours aimed to highlight whaling practices, they have moved to dispel this negativity, which is why I think they handed down this verdict."
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 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.
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.