Tokyo and Moscow are working to resolve decades of tensions over four islands occupied by the Soviet Union in the closing days of World War II and now controlled by Russia.
The man, who has not been identified, was detained following baggage checks conducted ahead of his scheduled departure, Chief Cabinet Secretary Yoshihide Suga told reporters.
Tokyo "strongly protested through diplomatic channels" and demanded he be allowed to return home, said Suga, who is the government's chief spokesman.
Ties have been strained for decades over the islands, known in Japan as the Northern Territories and in Russia as part of the Kuril Islands.
The dispute has prevented the two countries from signing a peace treaty to formally end wartime hostilities.
The detained man was a member of a visa-free visit programme that started in 1992, according to Suga.
The detention comes as Japanese Prime Minister Shinzo Abe and Russian President Vladimir Putin agreed in May to rekindle talks aimed at resolving the territorial dispute.
On Friday in Moscow, Chikahito Harada, Japan's special envoy for Japan-Russia relations, and Russian Deputy Foreign Minister Igor Morgulov will hold their second round of talks on the issue since the May bilateral summit.
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