The USGS put the epicentre of the shallow quake about 160 kilometres (100 miles) from the town of Makurazaki in southwest Japan, though no major damage was initially reported.
Tsunamis measuring one metre (three feet) in height were observed on several islands, public broadcaster NHK reported, citing local authorities, who were urging people in low lying areas to move away to higher ground for safety.
Authorities said larger tsunamis were still possible and urged caution more than an hour after the earthquake.
The Pacific Tsunami Warning Center had earlier said that there was no tsunami threat from the quake, which struck at 5:51 am (2051 GMT Friday).
Japan’s islands are situated at the juncture of several tectonic plates and experience a number of relatively violent quakes every year.
But building codes are rigorous and regular disaster drills are held, helping to ensure that despite their frequency and magnitude, quakes usually pass without loss of life or significant damage to property in Japan.
A massive undersea quake that hit in March 2011 sent a tsunami barrelling into Japan’s northeast coast.
As well as killing thousands of people and destroying communities, the waves also swamped the cooling systems at the Fukushima nuclear plant, sending three reactors into meltdown.
The nuclear disaster, the world’s worst since Chernobyl, displaced tens of thousands of people and rendered tracts of land uninhabitable, possibly for decades.
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