Foreign Minister Fumio Kishida said in a statement that Japan does not recognize the outcome of Crimea's referendum to split from Ukraine, saying it violates the Ukrainian constitution.
"It is regretful that Russia's recognition of the independence of Crimea interferes with the integrity of Ukraine's sovereignty and territory," Kishida told reporters.
"We cannot overlook Russia's attempt to change the status quo by force."
The moves are seen as mild compared to sanctions by the US and European Union, which have frozen the assets of individuals linked to the unrest in Crimea or who support the region's vote to secede from Ukraine.
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Ties between Russia and Japan have been strained for decades due to a dispute over a cluster of Russian-controlled islands off the northern island of Hokkaido called the southern Kurils in Russia and the Northern Territories in Japan. The dispute has kept the two countries from signing a peace treaty after World War II.
But last month, Prime Minister Shinzo Abe said that negotiations toward forging a treaty were accelerating. Abe is also eager to unleash new trade and energy business with Russia that has been hung up by the dispute.