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, citing internal policy, the AP reports.
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.
Public broadcaster NHK said the boats and their 11 crew members, who were unharmed, have been taken to nearby Shikotan Island , also part of the disputed island group. The boats were based in Rausu on the eastern coast of Japan 's northern main island of Hokkaido, it said.
Akira Muto, chief of the ministry's Russia section, called the incident "unacceptable," citing Japan's territorial claims over the islands and their waters. Muto also demanded Russian officials provide further details.
Russian Embassy officials were not immediately available for comment.
A bilateral fisheries accord allows only registered vessels to operate in the disputed waters. All 28 Japanese boats registered for the season's Okhotsk mackerel and octopus fishing were back in their ports Thursday, Fisheries Agency official Shingo Kurohagi said, indicating the seized boats might not have been covered by the pact.
Russia's ITAR-Tass news agency quoted Yevgeny Lazarev, spokesman for the Sakhalin regional office of the border guards service, as saying all four boats were seen violating the territorial limit. The trawlers were being taken to Yuzhno-Kurilsk on Kunashiri, although Russia spells the island Kunashir.
Russia seized the disputed island chain from Japan in the closing days of World War II. The dispute has kept the two countries from signing a formal peace treaty despite ongoing efforts by leaders from both sides to step up territorial negotiations.
Russian authorities have frequently seized Japanese boats in recent months as they have stepped up patrols in and around the area.
Last August Russian patrol boats fatally shot a Japanese fisherman and seized a vessel in the disputed northern waters, escalating tensions between the two nations.