Japan earlier said a Russian patrol boat opened fire on the Japanese vessel at about 2:25 a.m. Moscow time (10:25 p.m. GMT) Wednesday, 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 fired warning shots only after it refused to stop.
"The vessel did not respond to demands to stop, [and] it made dangerous maneuvers preventing an inspection team from approaching it," the FSB said in a statement, adding that the border guards shot two warning salvoes.
Russia's border guards, which were transferred to the FSB in 2003, often stop suspected poachers, including Russian crews, in the area.
"The crew [of the vessel] was trying to throw the [illegal] catch and fishing equipment overboard," the FSB statement said.
The agency said that after seizing the boat, a group of border guards found four fishermen, including the body of one man, more than three metric tons of crab and octopus caught without permission and crab traps aboard.
Deputy Ambassador Mikhail Galuzin was summoned Wednesday to the Japanese Foreign Ministry for an explanation.
"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 crew member, which is absolutely unacceptable."
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.
The Russian coast guard in the Far East confirmed that warning shots were fired at the Kisshin maru 31, but said the ship could have been hit inadvertently as the result of rough seas.
It is the third such incident for the Kisshin maru 31. It was involved in incidents with Russian coast guard in 1988 and 1994.
The vessel has been towed to the nearby port of Yuzhny-Kurilsk, where Russian military prosecutors will conduct an investigation into the shooting and the illegal border crossing, the FSB said.