He was formally arrested when the Shonan Maru 2 returned to its home port in Tokyo on Friday.
Sea Shepherd has Bethune boarded the ship to make a citizen's arrest in the latest incident in the group's long-running battle against Japanese whaling.
Masahiro Ichijo, a Japanese coast guard spokesman, said Bethune will be interrogated before prosecutors decide whether to press formal charges against him to stand trial in Japan.
|Sea Shepherd says Bethune had been trying to arrest the whaling ship's captain [AFP]
He said authorities were also considering additional allegations, including assault and destruction of property.
Japanese authorities say they suspect Bethune might be linked to the injury of two whalers hit by bottles containing rancid butter, and the slashing of a protective net belonging to one of the Japanese whaling boats.
Sea Shepherd said Bethune jumped aboard to make a citizen's arrest of its captain and hand over a $3m bill for the destruction of the Ady Gil, a high-tech protest ship Bethune captained, and which sank in January after colliding with the whaling ship.
Hirotaka Akamatsu, the Japanese fisheries minister, told reporters that Japan fully intended to press ahead with prosecuting the case.
"Anyone who has done wrongdoing will have to face severe punishment in accordance with the law," he said.
The protester regularly trail the Japanese whaling fleet, trying to disrupt the hunt by dangling ropes in the water to snarl the ships' propellers and hurling packets of stinking rancid butter on the whaling ships' decks.
|Japan maintains that it has the legal right to hunt whales for scientific research [AFP]
The Japanese whalers have responded by firing water cannons and sonar devices meant to disorient the activists.
Paul Watson, the founder of Sea Shepherd, told Al Jazeera the incident was going to make Bethune a national hero in his home country and neighbouring Australia.
"The issue is going to be a hot potato that Japan would not want to hold on to," he said, speaking from aboard the vessel Steve Irwin in Hobart, Tasmania.
"It is absurd they are charging him after his ship was rammed and sunk by the Shonan Maru, and that captain doesn't even get reprimanded.
Japan's annual whale hunt is allowed by the International Whaling Commission as a scientific programme, but critics call it a cover for commercial whaling, which has been banned since 1986.
Glenn Inwood, a spokesman for Japan's Institute of Cetacean Research, the body which oversees the annual whale hunt, said the annual whale research programme in the Antarctic is "purely legal, recognised and accepted" by the world whaling body.
"[Hunting] in the whale sanctuary is not a contravention of anything in the spirit of the sanctuary or in the legality of it," he told Al Jazeera.
"That is Japan's position… that it is quite clearly allowed in there under the convention."
He said Japan had undertaken the research to compile enough data so the International Whaling Commission can implement commercial whaling again.
"The idea here is for the resumption of commercial whaling in the Antarctic," he added.