A Japanese fisherman has been shot dead by a Russian patrol boat near a chain of disputed islands, the first fatality in 50 years, media reports said.
Japan summoned Russia's ambassador for an explanation
Japan's foreign ministry demanded the release of three other fishermen who were detained by the Russian boat.
Russia expressed regret but said the boat had entered its territory and said such breaches should not happen again.
Both sides claim the four islands, which Russia calls the southern Kurils and Japan the Northern Territories.
The dispute has stopped the two nations signing a peace treaty to end WWII.
The islands were seized by the Soviet Union at the end of the war in 1945. Russia has said it will hand over some of the islands to Japan, but Tokyo insists all four should be returned.
The Russian patrol boat opened fire on the Japanese vessel after it was found in Russian waters and refused to stop, according to Russian media.
The Russian coast guard insisted that the vessel defied several orders to stop and made dangerous manoeuvres, according to the Itar-Tass news agency.
The boat and its three remaining crew have now been taken to one of the disputed islands.
The BBC's Chris Hogg, in Tokyo, says fishing disputes are common in the area, and Russian border patrols often try to capture Japanese fishermen.
But the last time a Japanese citizen was shot dead by a Soviet vessel was nearly 50 years ago.