The Meteorological Agency said the offshore quake Sunday struck about 230 miles below the sea surface. The agency said there was no danger of a tsunami.
According to the U.S. Geological Survey, the earthquake struck about 300 miles south-southwest of Tokyo.
Buildings in the Tokyo area shook but there were no immediate reports of damage or injuries. Express trains in northern and central Japan were suspended temporarily for safety checks but later resumed.
No abnormalities were reported at power plants in the region, including the crippled plant hit by the March earthquake and tsunami, public broadcaster NHK reported.
Northeastern Japan was devastated by a massive earthquake and tsunami on March 11 that left nearly 20,000 people dead or missing. Japan, which lies along the Pacific "Ring of Fire," is one of the world's most seismically active countries.
The Associated Press contributed to this report.