Yasuhisa Shiozaki met with his Russian counterpart Alexander Alekseyev.
Earlier, a representative of the Japanese coast guard warned that bad weather could impede the return of a Japanese ship to its home port Friday.
Russia says 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.
Japan protested the death of the fisherman, which happened near the four Kuril Islands the country says are its "northern territories," and the seizure of the boat and the other crewmen and demanded their immediate release.
Relations between Russia and Japan have long been strained over the Kurils. Japan maintains that their seizure by the Soviet Union at the end of World War II was illegal, and the dispute has until now kept the two countries from signing a formal peace treaty.
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.
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.
