No injuries or casualties were reported after the 6.9 magnitude quake struck near Fukushima.
Japan has lifted all tsunami warnings which were issued after a powerful 6.9 magnitude earthquake hit the northeastern part of the country on Tuesday.
The quake struck near Fukushima prefecture at about 06:00 local time and was also felt in Tokyo, the Japan Meteorological Agency said.
Earthquakes are common in Japan, one of the world's most seismically active areas and the country accounts for about 20 percent of the world's earthquakes of magnitudes 6 or greater.
Earlier on Tuesday, tsunami warnings were issued after the agency said a 3.0 metre (9.9 feet) tsunami could hit the northeastern coast including Fukushima.
The area is home to the Fukushima Daiichi nuclear power plant which suffered a disaster after the tsunami of 2011.
Thousands of people were asked to evacuate the area and schools were closed.
Since 2011, all nuclear plants on the coast were shut down.
But, even after shutting down, plants still need cooling systems operational to keep spent fuel cool.
Only two reactors remain operational, both in the southwest of the country.