The quake hit at 3:03 am local time (1803 GMT Friday), the US agency said.
The USGS said the epicentre was 340 kilometres (211 miles) south of Kagoshima on Japan's third-largest island, Kyushu.
The epicentre was 17.5 kilometres below the surface, USGS said.
Minor tsunamis hit Japan late on dayWednesday following one of the biggest earthquakes in recent times near the north-eastern Russian-ruled Kuril islands.
The earthquake, which Japanese meteorologists gave a revised magnitude of 7.9, triggered alerts stretching from Indonesian to California. Japan lies at the junction of four tectonic plates and endures about 20 percent of the world's most powerful earthquakes, which frequently jolt Tokyo and other major cities.

Copyright AFP (Agence France-Presse), 2006