The quake was followed just over 20 minutes later by two aftershocks, a minute apart, of 5.6-magnitude
The quake hit at 3:19 am local time (1719 GMT Tuesday), 153 kilometres (95 miles) east of Chichi-shima in Japan's remote Bonin island region and at a shallow depth of just 14 kilometres.
There were no immediate reports of damage or injury.
The Hawaii-based Pacific Tsunami Warning Center said there was no threat of a destructive widespread tsunami.
But it warned in a bulletin: "Earthquakes of this size sometimes generate local tsunamis that can be destructive along coasts located within 100 kilometres of the earthquake epicentre.
"Authorities in the region of the epicentre should be aware of this possibility and take appropriate action."
Japanese television broadcasts carried a bulletin from the meteorological agency warning that a tsunami was expected to hit the coasts of Bonin island, referred in Japan as the Ogasawara islands, with two-metre (6.6-feet) waves predicted.
"Everyone near the coast must evacuate to a higher ground," the broadcasts warned.
The quake was followed just over 20 minutes later by two aftershocks, a minute apart, of 5.6-magnitude. Both were just 10 kilometres deep, USGS said.
Around 20 percent of the world's most powerful earthquakes strike Japan, which sits on the "Ring of Fire" surrounding the Pacific Ocean.
But high building standards, regular drills and a sophisticated tsunami warning system mean that casualties are often minimal.
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