The quake, at a shallow depth of 10 kilometres, struck shortly after 2:00 pm (0500 GMT) in Tottori prefecture.
Initially, the USGS had pegged the quake's magnitude at 6.6 before downgrading it.
Public broadcaster NHK quoted local officials as saying they had received reports that a house collapsed in the town of Yurihama, while fires broke out in another part of the prefecture, without giving details.
In Kurayoshi City, the fire department reported receiving seven emergency calls for injuries.
Television images showed severe shaking in the region.
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Bullet train services were suspended in the area, while nearly 40,000 homes were left without electricity as the quake damaged power lines, officials said.
NHK said switched-off nuclear reactors in the region were not affected.
Japan sits at the junction of four tectonic plates and experiences a number of relatively violent quakes every year, but rigid building codes and their strict enforcement mean even strong tremors often do little damage.
In April, two strong earthquakes hit southern Japan's Kumamoto prefecture followed by more than 1,700 aftershocks, and left at least 50 dead and caused widespread damage.
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