The Russian patrol shot the man after capturing a 4.9-tonne Japanese crab fishing boat in disputed waters off Japan's northern coast, said a spokesman for the Japanese coast guard.
Three more crew members were reportedly uninjured in the incident.
Kazuhiro Nakaya, a Japanese coast guard official, said special permission is needed to fish in the waters. It was unclear whether the Japanese fishing boat was operating properly at the time.
Japan summoned its Russian ambassador in protest at the incident and to demand the release of the remaining three fishermen.
Chikahito Harada, director-general of the foreign ministry's European affairs bureau, was quoted by the Japanese media as saying: "There is no way we can tolerate this unfounded situation to occur within Japanese waters."
The Russian ambassador later told journalists in Japan that the message would be conveyed to Moscow, but said the Japanese vessel was suspected to have been in Russian waters.
The boat was towed to one of the four Kuril islands off Japan's northern main island of Hokkaido for investigation by the Russian authorities.
The Kuril islands were seized by the Soviet army towards the end of the second world war and the Japanese residents expelled. However, Japan says the occupation is illegal and wants them returned.
The dispute has kept the two countries from signing a formal treaty ending wartime hostilities.
The islands are surrounded by rich fishing waters and are believed to have promising offshore oil and natural gas reserves, as well as gold and silver deposits.