The quake struck at 9:26 pm (1226 GMT) in Kumamoto, central Kyushu at a relatively shallow depth of 10 kilometres (6.2 miles), the Japan Meteorological Agency said.
Magnitude 6.7 earthquake jolts northern Japan, no damage from tsunami expected
The earthquake was felt throughout the southwestern island of Kyushu, Agency data showed, as media reported that shinkansen, or bullet, train service was halted.
There were no immediate reports of injuries but public broadcaster NHK showed some damage including broken concrete. Residents stood outside making calls on mobile phones.
Japan sits at the junction of four tectonic plates and experiences around 20 percent of the world's most powerful earthquakes.
6.1 quake hits off northern Japan
But rigid building codes and strict enforcement mean even powerful tremors frequently do little damage.
A massive undersea quake that hit on March 11, 2011, sent a tsunami barrelling into Japan's northeast coast, leaving about 18,500 people dead or missing, and sending several reactors into meltdown at the Fukushima nuclear plant in the worst atomic accident in a generation.
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