The boats were captured by the Russian border coast guard in the early hours off Kunashiri Island, one of four disputed islands between the countries, a Foreign Ministry official said on condition of anonymity.
Japan calls the island group the Northern Territories and Russia calls them the Kurils.
No other details were immediately known, the official said. He said the location and activity of the boats at the time of their capture were also unknown.
Akira Muto, chief of the ministry's Russia section, called the incident "unacceptable," citing Japan's territorial claims over the islands and their waters.
