A Russian patrol boat killed a Japanese fisherman today when it opened fire on a vessel in disputed waters in the Pacific ocean.

The crab fisherman, identified by Japanese media as Mitsuhiro Morita, 35, was shot in the head as he rushed to recover fishing equipment aboard the 4.9-tonne vessel Kyoshin Maru.

The incident took place near Kaigara island, one of several islands off the northeast tip of Hokkaido that are claimed by both Japan and Russia. It is the first fatal shooting in connection with the dispute in 50 years.

Three other crew members of the Kyoshin Maru were taken to nearby Kunashiri island, which is also in the southern Kuril chain and administered by Russia but claimed by Japan, for further investigation, according to news reports. They were not injured but may face criminal charges, according to NHK, a Japanese television channel.

Russia expressed regret over Morita's death, but said that the boat was to blame for violating its waters, and warned Japanese vessels to stay out.

The Japanese government expressed outrage..

"There has been a loss of life, and the situation is grave. Japan demands an immediate apology," said Taro Aso, the Japanese Foreign Minister, after a tense meeting with Russian Deputy Ambassador Mikhail Galuzin in Tokyo. "It’s unacceptable this took place within Japanese waters."

The Foreign Ministry released a statement demanding immediate compensation and the release of the boat and surviving crew. It called on Russia take measures to prevent similar incidents.

Russian officials defended the patrol boat’s actions, insisting that the Japanese ship had violated Russian waters and that authorities acted within their powers.

The responsibility for the shootings lay instead "with the direct culprits and ... with Japanese authorities that close their eyes to fishermen’s poaching in Russian territorial waters," Russia’s Foreign Ministry said in a statement, which nonetheless went on to express regret over the death.

Morita’s mother, Shoko, said from her home in Hokkaido that she couldn’t believe her son was dead.

"I don’t understand why they had to open fire," Shoko said through tears on NHK. "He was a good son. He didn’t do anything wrong."

The disputed waters lie around four islands, called the Kurils in Russia and the Northern Territories by Japan, which were claimed by the Soviet army near the end of the Second World War. Tokyo has demanded their return, and the dispute has blocked a treaty formally ending wartime hostilities.

While Russian authorities have seized dozens of Japanese boats and injured several fishermen over the years, this was the first shooting death of a Japanese since October 1956, Coast Guard officials said.

Japan’s Fishery Agency acknowledged that crab fishing in that area is illegal, though it said it was unclear whether the boat was illegally fishing at the time of the shooting.

The Japanese Foreign Ministry officials insisted the boat was in Japanese waters. Japan's coastguard service said that it had sent two vessels to the scene to investigate.

A total of 30 fishing boats and 210 Japanese crew members were seized by Russia in the disputed northern waters between 1994 and 2005, while seven other fishermen were injured when the Russian coast guard fired at them during the same period, according to the Japan Coast Guard.

The islands are surrounded by rich fishing waters and are believed to have promising offshore oil and natural gas reserves, as well as gold and silver deposits.

President Putin has offered to revive a 1956 Soviet-Japanese declaration under which Moscow had agreed to return two of the islands, but Tokyo rejected the proposal as insufficient and talks on the issue are deadlocked.

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