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, an interpreter who has not been identified, was visiting Kunashiri - Kunashir in Russian - one of the islands off northern Japan, as part of a visa-free visit programme that started in 1992.
The man was detained by Russian customs ahead of his scheduled departure and accused of trying to take cash off the island illegally, a Japanese ministry official said.
The man had claimed that he was asked by a local resident to carry a package but was unaware it was cash, the official said.
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"After questioning, he was found innocent," the official told AFP on customary condition of anonymity, adding he was released yesterday.
"We understand the Russian authorities have accepted his claim."
The Japanese government - which had lodged a diplomatic protest - is arranging for the man to return to Nemuro port on the country's northern main island of Hokkaido on Monday, he said.
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, Japan and Russia are scheduled to hold their second round of talks on the issue since the May summit.
Some Japanese media speculated that the man's fairly quick release came as the Russian side possibly tried to limit the diplomatic impact of the case.