A row broke out between Moscow and Tokyo after Japan accused the border guards of shooting dead a Japanese crewmember on a fishing vessel allegedly poaching in Russian territorial waters.
"The procedure for visa-free travel between northern Hokkaido and the Sakhalin Region will remain unchanged," a ministry spokesman said.
The statement came in response to comments made by Hiroshi Fujiwara, the mayor of Hokkaido, the second largest of Japan's four main islands. He demanded Wednesday that the visa-free regime be scrapped with the Sakhalin Region and aid to residents of the South Kuril Islands should be stopped.
The Japanese Foreign Ministry official said the visa-free regime was a very effective method of resolving the territorial dispute between Japan and Russia.
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.
