Tokyo's move comes amid signs of tension between the two nations over their own territorial dispute. The additional sanctions curtail the activities of Russian banks in Japan and increase controls on arms exports.
It is to be noted that earlier lighter sanctions were adopted by Japan than the US and its allies as it did not want to derail improved relations with Russia.
Chief Cabinet Secretary Yoshihide Suga said the new measures put the emphasis on Japan's co-operation with other members of the G-7, whose foreign ministers meet on the sidelines of the UN General Assembly in New York this week.
Suga made the statement immediately after he had protested to Moscow over the visit by a senior Russian official to disputed islands seized by the Soviet Union at the end of World War Two. "A visit like this hurts the Japanese people's feelings and is extremely regrettable," he said.
The official Sergei Ivanov, a close aide of President Vladimir Putin, visited a new airport on one of the disputed islands off Hokkaido, known as the Northern Territories by Japan and the Southern Kurils by Russia.
For his part, Japanese Prime Minister Shinzo Abe has made several efforts to strengthen relations with Putin since taking office in 2012, meeting the Russian leader on five occasions.
Japan is interested to improve economic co-operation, given its interest in Russian natural gas reserves.
Meanwhile, Russia has responded strongly to Japan's move saying: "We regard this unfriendly step as yet another sign of Japan's incapability of building up its foreign policy on its own."
"Tokyo is doing damage to its own geopolitical positions and is sending a wrong signal to its business community," continued the statement.
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