The Kremlin said talks set for Thursday will focus on "the state and prospects for development of Russo-Japanese cooperation in the political, trade and economic, and humanitarian spheres."
The meeting follows on from Putin's first visit to Japan in 11 years last December, when the two leaders failed to resolve a disagreement over an island chain that has prevented their nations signing a peace treaty to formally end World War II.
The Soviet Union seized islands off Japan's northern coast in 1945 in the closing days of the war.
Known as the Southern Kurils in Russia and the Northern Territories in Japan, they have been a thorn in relations ever since.
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