The quake struck at 8:48 am (2348 GMT Thursday) in Pacific waters nearly 40 kilometres (25 miles) east-southeast of Miyazaki city at a depth of 24 km, according to the agency.
The Japan Meteorological Agency said there were no worries about tsunami damage.
The weather agency issued an emergency warning when the quake hit, prompting public broadcaster NHK to switch to special programming on the situation in the southern Kyushu region, including Miyazaki.
The initial quake was followed by another, of 5.1 magnitude, at 9:07 am (0007 GMT) in the same area, according to the USGS.
Local media reported no damage in Miyazaki and its surrounding areas.
Japan sits at the junction of four tectonic plates and experiences a number of relatively violent quakes every year.
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