An earthquake measuring about 7.3 on the Richter scale shook western Japan on Sunday, the second strong quake to hit the area in five hours, and evacuations were ordered as tsunamis approached the coast, NHK television said.
The Japan Meteorological Agency said tsunamis measuring up to 2 metres (6 feet) high could hit some areas of the Pacific coast, and some measuring less than 1 metre had already struck.
Residents of Owase City in Mie Prefecture were ordered to evacuate to higher ground to avoid the tsunamis - water waves generated by seismic activity - and there were reports of fishing boats being overturned in the town's harbour.
Television pictures showed residents leaving home, carrying children and belongings.
NHK said at least seven people had been injured in the latest quake, which struck at 11:55 pm (1455 GMT).