Speaking to reporters at her office in Tokyo, Japanese Prime Minister Sanae Takaichi said the extent of casualties and property damage was being assessed.
"We have already been informed that people have been injured," Takaichi said on Tuesday.
"Power outages and fires have occurred in some areas, and there has also been damage to roads and bridges and the collapse of buildings.
"Above all, I ask everyone to take action to protect themselves, including evacuating to a safe location."
Public broadcaster NHK showed several buildings on fire or collapsed, large cracks along roads, including an elevated highway, and a derailed goods train.
More than 150,000 people were instructed to go to evacuation centres, the disaster management agency said.
TSMC, the world's largest contract chipmaker, evacuated workers from its plant in the area as a precaution, a spokesperson for the firm said.
A spokesperson for electronics firm Sony, which also has a plant there, said it was checking the situation.
Residents in the areas that felt the biggest tremors must beware of further strong quakes for about a week as well as the risk of landslides, an official for the Japan Meteorological Agency (JMA) said.
The Japanese government issued emergency earthquake warnings for Kumamoto, Nagasaki, Kagoshima, Fukuoka, Saga, Oita, and Miyazaki prefectures, all on Japan's southern Kyushu island.
The JMA also initially issued a tsunami warning for a wave measuring one metre but later lifted it.
Japan is one of the world's most earthquake-prone countries, with a tremor occurring at least every five minutes.
Located along the "Ring of Fire" of volcanoes and oceanic trenches partly encircling the Pacific Basin, Japan accounts for about 20 per cent of the world's earthquakes of magnitude 6.0 or more.
Kyushu Electric Power said about 40,000 homes had lost power as a result of the latest quake, while railway company JR Kyushu said it had suspended services, including its high-speed bullet trains.
Kumamoto airport also shut its runway, as airlines diverted and cancelled flights.
Telecoms operators KDDI and Docomo said there was disruption to their mobile phone services due to power shortages and transmission-line failures.
There were no irregularities reported at the nuclear power stations in the area, Japan's nuclear regulation authority said.
A massive earthquake in Kumamoto 10 years ago killed 275 people and injured a further 2739, according to an official count, and damaged thousands of buildings including the city's castle, a top tourist site.
