Ady Gil, the Sea Shepherd's powerboat, was sliced in two in a collision with the harpoon boat in January.
Bethune had said he boarded the harpoon boat to make a citizen's arrest of the captain, for what he said was the attempted murder of his six crew, and to present him with a $3m bill for the destruction of the powerboat.
"Bethune inflicted a chemical burn on a Japanese whaler's face by hurling a bottle of butyric acid which smashed aboard the Shonan Maru II days before he boarded the ship," the prosecution brief said.
The Sea Shepherds described the bottles as containing "rancid butter stink-bombs".
Bethune faces assault and business obstruction charges, which each carry prison terms of up to 15 years or fines of up to $5,000.
"Our country will deal strictly with such cases under the law," Hirofumi Hirano, Japan's chief cabinet secretary, said, denying any plans to hold negotiations with the activist group.
The Sea Shepherds urged Australian police to prosecute the captain and crew of the harpoon boat over the collision and have described Bethune as a "political prisoner".
Commercial whaling was banned under a 1986 moratorium, but Japan still hunts whales for what it says are scientific research purposes.
Japan maintains that whaling has been part of its culture for centuries, and does not hide the fact that whale meat ends up in shops and restaurants.
The Sea Shepherd sends vessels to confront the fleet each year, trying to block the whalers from firing harpoons.
The whalers respond by firing water cannons and sonar devices meant to disorient the activists.
Clashes between the anti-whaling protesters and Japan's whaling fleet in Antarctic waters became increasingly confrontational this year, when the Sea Shepherd protest boat was sliced in two by the bow of a whale boat.
Australia has threatened to take Tokyo to the International Court of Justice unless it ceases its annual whale hunts by November. Some legal experts say Japan's hunt breaches international laws such as the Antarctic Treaty System.
A court challenge would lead to provisional orders for Japan to halt whaling immediately ahead of a full hearing.