The former activist of the US-based Sea Shepherd Conservation Society, has been held in custody since February after he boarded the Japanese whaling fleet's security ship the Shonan Maru II during its annual whaling hunt in southern waters.
Protests were under way outside the Tokyo District Court in advance of the sentencing, with some placards branding the New Zealander as a "racist and eco-terrorist".
One of Bethune's lawyers, Dan Harris, told the Australian Broadcasting Corporation he had been hoping his client would get a suspended sentence and will be released - but said the New Zealander had still steeled himself to serve a jail term.
"I would say he is ... prepared for a long jail term, to the extent anyone's prepared," he said, before the sentencing. He noted that jail meant being moved from the city's detention centre into a fully fledged prison: "and Japanese jails are not good places to be" .
Bethune's wife, Sharyn, earlier said that she was looking at taking his two teenage daughters, Danielle, 15, and Alycia, 13, to visit him in jail if it turned out that he was required to serve a long jail sentence.
He admitted four charges of obstructing commercial activities and trespass, vandalism and carrying a knife, which he used to cut security netting on the whaling ship he boarded.
But Bethune denied a charge of assault, in which prosecutors said a 24-year-old whaler suffered chemical splash burns to his face during a February 11 confrontation in which Sea Shepherd activists hurled butyric acid stink bombs.
"I did not have the intention of hurting crew members. I took action because I wanted to stop Japan's illegal whaling," Bethune said in his final statement last month, which he tearfully delivered in Japanese.
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.
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 said reduced the Japanese cull by several hundred whales.
The New Zealander was captain of the group's futuristic carbon-and-kevlar powerboat, the trimaran Ady Gil - formerly his round-the-world record-setting trimaran Earthrace - which sank after a January 6 collision with the fleet's security ship.
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 $US3 million bill for the Ady Gil.
Instead, he was detained and taken back to Japan, where he was formally arrested on March 12 and has been in detention since.
