The epicentre of the quake - which struck at 2:06 am (1706 GMT) - was located 13 kilometres north of the city of Kunisaki-shi, USGS said.
The quake struck at a depth of 82 kilometres.
There was no immediate warning message issued by the Pacific Tsunami Warning Center.
More than 18,000 people died when a 9.0-magnitude undersea earthquake sent a towering tsunami barrelling into Japan's northeast coast in March 2011 in the country's worst post-World War II disaster.