Russia said earlier, Mitsujiro Morita, 35, the sailor from the fishing boat suspected of poaching crab in the Pacific waters, which both Russia and Japan claim as part of their territory, 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 on Wednesday.
The fisherman's body was handed over to a Japanese delegation at 05.20 Moscow time (01.20 GMT) on the island of Kunashir (southern Kurils).
The Russian 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.
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.