The earthquake struck at 7:42 am (2242 GMT Friday) eight kilometres east-northeast of the city of Miyako at a depth of 44 kilometres, the US Geological Survey said.
The Japan Meteorological Agency measured it at 5.8 and said there was no risk of a tsunami.
Japan is situated at the conjuncture of several tectonic plates and experiences a number of relatively violent quakes every year.
But thanks to strict building codes, even powerful quakes that might wreak havoc in other countries frequently pass without causing much damage.