A spokesman for the Japanese Foreign Ministry said the Russians handed over the detainees during a meeting aboard a Japanese fisheries patrol boat near Kunashiri Island.
The spokesman said the captain, who has reportedly assumed all blame for his boat's alleged violation of Russian territory, will remain in Russian custody for the time being.
On August 16, a Russian coast guard boat fired at a Japanese vessel that was allegedly trespassing in Russian waters off Japan's northernmost main island of Hokkaido, killing one Japanese crab fisherman.
Russian authorities seized the fishing boat, along with its captain and the two crew members.
The incident occurred near a disputed chain of islands that have been controlled by Russia since the end of World War II. The islands are known in Russia as the Southern Kuriles and in Japan as the Northern Territories.