Japan accused the border guards of shooting dead a Japanese crewmember on a fishing vessel allegedly poaching in Russian territorial waters on Wednesday.
But Vyacheslav Dorokhin, the first deputy head of the FSB border service, said, "Russian border guards followed to the letter everything set out in international and Russian law [to detain a ship suspected of crossing a border illegally]."
The FSB assumed responsibility for Russia's border guards in 2003.
The Russian Foreign Ministry said earlier in the day Japanese Deputy Foreign Minister Yasunori Shiozaki would arrive in Moscow Friday at the urgent request of Japan to coordinate procedures to hand over and receive the body of 35-year-old Mitsujiro Morita.
The Russian Foreign Ministry suggested after the incident that the seaman could have been hit by a bullet inadvertently as the result of rough seas when a patrol boat fired warning shots after the ship had defied orders to stop.
He said the border guards had fired six green rockets in pursuit of the vessel as a signal for it to stop. They also used a special radio communication channel with the Japanese vessel and demanded that the Japanese captain stop the vessel.
"The blame for the accident lies with nobody but the captain [of the vessel]," Dorokhin said. He added the captain had already admitted that he was in Russia's territorial waters and was in breach of Russian legislation.
The incident could mar relations for some time - particularly as the death happened near four Kuril islands that Japan claims as its "northern territories" - Foreign Ministry spokesman Noriyuki Shikata said Thursday: "Russia's refusal cooperate [on the release of the ship and crew] could affect further relations between our countries."
Russia's prosecutors in the Far East have opened investigation against the crew on illegal-border crossing and poaching charges, which could mean crewmembers facing two to five years in prison and a substantial fine or 18 months in prison respectively, according to the popular Russian daily Kommersant.
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.
Russia's Foreign Ministry said it regretted the death of the fisherman, but added responsibility also rested with some representatives of the Japanese authorities for failing to address the poaching problem after Moscow had repeatedly highlighted it.
