Noboru Sakashita, 59, was arrested August 16 near the Kuril Islands in an incident that saw one of his crewmates fatally shot by Russian border guards. Russian officials said the vessel was suspected of illegally fishing for valuable crab in Russian territorial waters, and that border guards had fired warning shots only after it had refused to stop.
The Japanese captain has been charged with illegally crossing the Russian border and illegally fishing in Russian territorial waters, the Prosecutor General's Office said. He is facing a cumulative fine of about 500,000 rubles ($18,500), or up to two years in prison.
Earlier Sakashita took responsibility for the alleged poaching incident while being questioned by Russian authorities, saying the crewmembers on the Kisshin maru 31 had been unaware they had crossed Russia's maritime border.
The other two fishermen on the vessel at the time of the incident were released August 30 and handed over to Japan by Russian authorities.
The incident strained relations between Russia and Japan, who have contested the ownership of the Kurils for over 60 years. Japan maintains that their seizure by the Soviet Union at the end of World War II was illegal, and the dispute has until now kept the two countries from signing a formal peace treaty.