A row broke out between Moscow and Tokyo after Russia shot dead a Japanese crewmember on a fishing vessel allegedly poaching in Russian territorial waters.
"The Russian Foreign Ministry deeply regrets the death of one of the crew members," the ministry said in a statement.
Japan said a Russian patrol boat opened fire on the vessel at about 2:25 a.m. Moscow time (10:25 p.m. GMT), killing one man aboard. Russian officials said the vessel was suspected of illegally fishing for valuable crab in Russian territorial waters, and that border guards had fired warning shots only after it refused to stop.
"Obviously, the responsibility totally rests with the direct culprits, and also with those representatives of the Japanese authorities who turn a blind eye to poaching in Russian territorial waters by Japanese fishermen," the statement said.
Crab fishing in the area, which is administered by Russia but claimed by Japan, is illegal, although it is unclear whether the vessel was fishing at the time of the incident.
Japanese Foreign Minister Taro Aso said he would personally speak to his Russian counterpart by telephone to protest.
"This is an extraordinary incident given our position on the territorial dispute between Japan and Russia," a Japanese foreign ministry official said earlier. "It led to the death of a crewmember, which is absolutely unacceptable."
The Russian ministry said it had called on the Japanese authorities to address the issue of Japanese poachers in Russian waters many times.
"Russian authorities have repeatedly drawn the attention of Japanese officials to the increasing incidence of poaching involving Japanese fishermen in Russian territorial waters, and have asked that the issue be resolved," the ministry said, adding that the requests had been ignored.
The ministry said the Japanese fishermen had refused to obey an order to stop.
"The violators tried to escape, engaging in dangerous maneuvers and trying to ram the patrol boat when officers tried to board the [fishing] vessel for inspection," it said.
Tatyana Kutuzova, an aide to the regional prosecutor on the island of Sakhalin, said earlier Wednesday that the Japanese vessel had entered Russian waters without identification markings, and that 30 kilograms of crab and 10 kilos of octopus was found on board. Russian diplomatic officials confirmed earlier reports that the crewmen had been throwing the catch overboard as they fled the coastal patrol.
The Russian coast guard in the Far East said that warning shots had been fired at the Kisshin maru 31, but said the ship could have been hit inadvertently as the result of rough seas.
The ministry said the boat was currently at the Yuzhnokurilsk port on Kunashir Island, one of the Kuril Islands claimed by Japan. Japan's consulate general in Yuzhno-Sakhalinsk on Sakhalin Island has been informed of the incident.
Following the incident, Deputy Ambassador Mikhail Galuzin in Tokyo was summoned to the Japanese Foreign Ministry for an explanation.
The head of the European Affairs Bureau at the Japanese ministry, Tikahito Harada, issued a protest and demanded the immediate return of the Japanese vessel and the body of the fisherman, but Russian officials have so far refused.
Relations between Russia and Japan have long been strained over the Kuril Islands. Japan maintains that their seizure by the Soviet Union at the end of WWII was illegal, and the dispute has until now kept the two countries from signing a formal peace treaty.
It is the third such incident for the Kisshin maru 31. It was involved in confrontations with the Russian coast guard in 1988 and 1994.
A total of 30 fishing boats and 210 Japanese crewmembers were seized by Russia in the disputed waters between 1994 and 2005. Seven fishermen were injured when Russian patrolmen fired on them.