Following the quake, tsunami warnings were issued but these were subsequently retracted.
The two countries have been locked in a territorial dispute over a remote island chain since the end of the conflict.
Moscow has ignored Japan's qualms about warplanes on an island Tokyo claims, promising to keep it informed about "everything that happens on the territory of Russia."
Both Russia and Japan claim the so-called Kuril Islands, in a dispute stretching back to World War Two.
Moscow repeatedly called for the U.S. to step back from its military reinforcement of Japan and South Korea in response to Pyongyang's nuclear tests.
Russia and Japan have argued about a stretch of islands for over 60 years, but this is not stopping Moscow from raising military compounds on it.
The Japanese PM's approval rating fell by 6 percent in a month.
This is why Russia and Japan still have no World War II peace deal.
Japan and Russia have still not signed a World War II peace accords due to the dispute.
Russia and Japan have pursued a diplomatic solution, but Moscow is shoring up defenses.
Japanese Prime Minister Shinzo Abe said all four disputed islands belong to Japan.
Japan has made territorial claims on the islands since the 19th century.