New Zealander Peter Bethune climbed onto the Shonan Maru 2 from a Jet Ski in February in what he said was an attempt to confront the ship's captain over the sinking of a protesters' vessel the previous month.
Prosecutors say Bethune threw glass bottles containing rotten butter at the harpoon boat, including one that broke and left three Japanese crew members with chemical burns. He was apprehended when the ship returned to Tokyo in March.
Bethune, 45, is charged with trespassing, vandalism, possession of a knife, obstructing business and assault. He pleaded guilty to all but the assault charge when his trial started last month.
At Tokyo District Court on Thursday, prosecutors said there was a "clear link" between his firing of the bottles and the injuries and that he must have been aware that a bottle might hit a crew member.
Prosecutors also said Bethune "actively took part and carried out actual attacks" as part of a violent campaign against Japanese whaling by Sea Shepherd, the U.S.-based conservation group to which he once belonged.
Bethune's lawyers sought lenience and a suspended prison term, saying Thursday that he participated in protests "purely out of his sense of justice."
Thursday's session wraps up the proceedings ahead of a ruling expected on July 7.
During earlier trial sessions, Bethune said he just wanted to confront the ship's captain and hand him a $3 million bill for the destruction of a protest ship that sank during a collision in January. He denied any intention to hurt anyone.
In his tearful closing statement, Bethune apologized for the trouble but said he never intended to hurt anyone.
"I took action because I wanted to stop Japan's illegal whaling," Bethune said, as he read his statement in Japanese. "But I feel sorry for having caused trouble to crew members."
"I am not apologizing because I am trying to lessen the charges," he said with his voice trembling, choked with tears. "I did not intend to injure the crew members of Shonan Maru."
Sea Shepherd said it expelled Bethune because he violated its policies against carrying weapons. The group said he had a bow and arrows with him while he was aboard the Sea Shepherd vessel Ady Gil, the one that was destroyed, although he never used them and the group believes he never intended to use them.
The bow and the arrows were never discussed during Bethune's trial.
In his court appearances last month, Bethune said he will likely no longer continue his anti-whaling protests.
The Sea Shepherd group has been protesting Japan's government-backed research whaling program for years, often engaging in scuffles with Japanese whalers.
Japan joins Norway and Iceland in hunting whales under exceptions to a 1986 moratorium by the International Whaling Commission. Japan says it hunts for scientific research and is legitimate under IWC, but opponents call it a cover for commercial whaling. Japan's whaling program also involves large-scale expeditions down to the Antarctic, while other whaling countries mostly stay along their coasts.
Sea Shepherd leader Paul Watson said in a statement Wednesday that his group will continue to support Bethune through his court battle in Japan. He denied Japanese prosecutors' allegations that he had ordered Bethune to climb onto the Japanese whaling vessel.
About 30 Japanese rightists staged a rally outside the court, shouting through a loudspeaker, denouncing Bethune and Sea Shepherd. They confronted Garry Thomason, Bethune's fellow activist, prompting Japanese police to pull him away for protection. Nobody was injured or arrested.