Mr. Bethune was taken into custody by the crew, who held him for a month as the whaling ship returned to Japan. When the boat arrived in Tokyo on March 12, he was taken into custody by the Japanese Coast Guard.

The Ady Gil was being used by the Sea Shepherd groupto interfere with Japanese whaling ships during their annual hunt in the Antarctic, south of Australia and New Zealand. The bow of the Ady Gil was sheared off in the collision, and Mr. Bethune and his crew were rescued by the Bob Barker, another Sea Shepherd boat.

Each ship blamed the other for the incident.

The assault and obstruction of business charges carry prison terms up to 15 years, and a trespassing conviction can result in a three-year prison sentence, The Associated Press reported from Tokyo.

Japanese media reports have suggested that Tokyo intends to use Mr. Bethune’s case as a warning to Sea Shepherd to end its confrontations with Japan’s whaling fleet. The group has tried to disrupt the Antarctic hunts by blocking Japanese ships, using ropes to clog their propellers and throwing bottles of rancid butter onto their decks to make them slippery.

Hirotaka Akamatsu, the Japanese fisheries minister, told reporters when Mr. Bethune was arrested that his actions were “outrageously illegal behavior.”