Russia and Japan have yet to sign a formal treaty ending World War II hostilities, due to their territorial dispute over the four South Kuril Islands, former Japanese territory annexed by the Soviet Union after the war.
"This [peace treaty] can only be done in a way that will meet the national interests of the Russian Federation," Putin told reporters.
He said the content of a peace treaty would be a focus of future bilateral negotiations.
The premier said on Tuesday that President Dmitry Medvedev would discuss territorial issues and a formal peace treaty with Japanese Prime Minister Taro Aso at the upcoming G8 summit in Italy.
Putin visited Tokyo on Tuesday to discuss the long-standing dispute, along with economic, energy and international issues.
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Ukraine has not preserved its 1991 borders. The signing of the Geneva memorandum on April 17 reaffirmed the willingness of Russia, the United States and EU countries to reach a compromise. While the sides continue to trade tough talk and symbolic sanctions, the Kremlin and the White House are also holding a parallel dialogue on the coordinated geopolitical revision of Eastern Europe.