The epicentre of the earthquake was 155km (95 miles) off the Bonin Islands, some 1,000km south-east of Tokyo, the USGS said.
It struck at a depth of some 15km at 0220 (1720GMT), sparking local tsunami warnings which were later lifted.
Japan is well-prepared for quakes which often hit the seismically active area.
In 1995, a magnitude-7.2 quake in the port city of Kobe killed 6,400 people.
There were no reports of casualties or damage from the latest earthquake.
Local TV broadcasts warned coastal inhabitants to seek safety on higher ground, but the quake only prompted a swelling of waves around 30cm (1ft) high.
Known in Japan as the Ogasawara Group, the Bonin archipelago comprises some 30 tropical or sub-tropical islands, only two of which are populated.
They are inhabited by around 2,500 people – BBC news