The quake struck at 5:33 a.m. about 6 miles from Sumoto on Awaji Island, USA Today reported. It had a depth of 3.3 miles.
The Japan Meteorological Agency said at least eight 3.0-magnitude aftershock tremors were registered within 90 minutes of the initial quake.
At least eight people suffered minor injuries due to the quake but there were no immediate reports of structural damage, RIA Novosti reported.
Air and rail transport in the area of the quake was halted briefly, but has since resumed, officials said.