A Japanese whaling vessel and its crew were being held in Russia on Friday after the ship entered Russian territorial waters without permission, Tokyo said.

The 712-tonne Shonan-maru No.2 was ordered into a Russian port on August 15 after sailing through the Sea of Okhotsk off Sakhalin island, an official from Japan's Fisheries Agency said.

The vessel, which does not catch whales itself but monitors the oceans for signs of the creatures, had 19 Japanese crew and one Russian observer on board.

Tokyo has admitted the vessel changed its initial course and entered Russian waters without going through the proper procedures.

"The crew members have been voluntarily questioned," the official said, adding that Tokyo was asking for their early release through diplomatic channels.

Ties between Japan and Russia have warmed in recent years after decades of mistrust over disputed territory taken by Soviet troops in the closing moments of World War II.

But the relationship has soured as Tokyo has joined its Western allies in imposing sanctions on Russia in the wake of its annexation of part of Ukraine.

Earlier this month Moscow scrapped a meeting with a Japanese minister in response to a new round of sanctions against senior figures in the Russian government.

The meeting, originally scheduled for late August, was expected to focus on the simmering territorial dispute. Japan is a close ally of the United States, which has been piling pressure on Russia over its involvement in Ukraine.

Last week Japan lodged a "stern" protest with Russia over military exercises that are being held on the disputed Kuril islands.

Both Moscow and Tokyo had hoped to start mending relations in order to revive trade, with Japan seeking broader access to Russia's plentiful oil and natural gas supplies.

Russian President Vladimir Putin hosted Japanese Prime Minister Shinzo Abe in April 2013 for the two sides' first formal summit in Moscow in a decade.

The leaders agreed to set in motion a series of high-level talks about Tokyo's claim to the southern Kuril chain that it still refers to as the Northern Territories.

Japan said last month it had wrapped up a whale hunt in the Pacific, the second campaign since the UN's top court ordered Tokyo to halt a separate slaughter in the Antarctic.

The Shonan-maru No. 2 has previously been used during the now-suspended Antarctic whaling hunt, during which there have been clashes with environmentalist groups.