The quake, which the US Geological Survey measured at 6.0, 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.
The quake was followed about 30 minutes later by another smaller one with a magnitude of 5.7, the agency said. That quake also did not generate a tsunami warning.
Japan's public broadcaster NHK reported that some buildings had collapsed on Kyushu with people possibly trapped, though details were scarce.
Cameras set up by NHK showed violent shaking at the time of the quake, which was felt throughout Kyushu.
Japanese media reported that shinkansen, or bullet, train service was halted on the island.
NHK showed some damage including broken concrete. Residents stood outside making calls on mobile phones.
An official at the Sendai nuclear plant in Kyushu, who declined to be named, said the plant was operating normally but that officials were checking for any abnormalities.
Japan sits at the junction of four tectonic plates and experiences around 20 percent of the world's most powerful earthquakes.
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.