There were no immediate reports of damage or injuries, but the Meteorological Agency warned that tsunamis - water waves generated by seismic activity - could hit broad areas on the Pacific Coast in central to western Japan, NHK said. The broadcaster said a tsunami measuring up to 1 meter (3 feet) may have already hit the Pacific coast.
The quake was felt just before midnight (1500 GMT).
Earlier in the evening, an earthquake measuring 6.9 on the Richter scale hit western Japan on Sunday, setting off tsunami waves along the Pacific coast, but there were no reports of serious damage, NHK said.
Two people were slightly injured in the city of Kyoto, although some of the strongest tremors were felt in the area of Nara, the ancient capital of Japan where there are many temples.
Tsunamis measured up to 50 cm (20 inches) in some areas, the Japan Meteorological Agency said.
The agency initially said the quake measured 6.8 on the Richter scale and estimated the largest tsumani at 60 cm.
Train services including bullet-train runs were temporarily suspended after the quake struck shortly after 7 p.m. (1000 GMT).
The focus of the quake, which measured five on the Japanese intensity scale of seven, was in the seabed off the Kii Peninsula about 500 km (310 miles) southwest of Tokyo at a depth of about 10 km (6 miles), the Japan Meteorological Agency said.
Authorities lifted tsunami warnings about two hours after the quake, which was also felt in Tokyo, and said there was no worry about damage to coastal areas.
Much of the affected area relies on fishing and agriculture as well as tourism, centered on Nara and Kyoto.
Japan is one of the world's most seismically active areas, with an earthquake occurring every five minutes.
The country accounts for about 20 percent of the world's earthquakes of magnitude six or greater. A quake of that magnitude has potential to cause major damage in built-up areas.
Memories are still vivid of the earthquake in the western city of Kobe which killed more than 6,400 people in 1995. That quake measured 7.2 on the Richter scale.