The authorisation on Saturday "for use of the armed forces of the Russian Federation in Ukraine heightens the tension in the region and would harm the peace and stability of the international community," it said.
"In this regard, Japan expresses grave anxiety and concern over the decision," it said.
"Japan strongly expects that the situation in Ukraine will be settled in a peaceful manner and strongly urges all the parties concerned to behave with maximum self-restraint and responsibility, to fully observe the relevant international laws," the foreign ministry statement said.
The comments come in parallel to a statement from the G7 condemning Russia's "clear" violation of Ukraine's sovereignty. Japan is a member of the grouping.
Criticism of Moscow is a difficult balancing act for Tokyo, at a time of warming relations between Prime Minister Shinzo Abe and President Vladimir Putin.
Abe was one of the few pro-Western leaders who attended the opening ceremony of the Winter Olympics in Sochi. Many others stayed away amid disquiet over anti-gay laws.
The two men also held a meeting during the visit, their fifth one-on-one since Abe came to power in December 2012.
Japanese officials have said building trust between the leaders is important for progress towards a peace treaty that has still not been signed more than 68 years after World War II hostilities ceased.
The two sides remain at odds over islands to the north of Hokkaido that were seized by Soviet forces in the last gasps of the conflict.
Economic ties between Moscow and Tokyo have in recent years expanded. chiefly in exports of Russian natural gas to resource-poor Japan but also through Japanese companies' investment in Russia.
Some commentators had said the two sides looked set to go a long way to solving the islands dispute over the coming months. That progress may now be iced, with Japan expected to fall into line with the US, its guarantor.
The possible stalling of progress on what Japan calls the Northern Territories, which Russia administers as the Southern Kurils, would mark a frustration for Abe, who is eager for a foreign policy victory at a time of fractious disputes over territory and history with China and South Korea.
The row with Beijing is particularly nasty and frequently involves paramilitary stand-offs, with some commentators warning it could degenerate into armed confrontation that might drag the United States in.