Speaking to reporters at her office in Tokyo, Japanese Prime Minister Sanae Takaichi said the full extent of casualties and damage from the 7.1 magnitude quake was still 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."
One hospital had reported more than 50 injuries, public broadcaster NHK said.
Several people on a high-speed train at the time of the quake were also injured, Nikkei newspaper said.
Multiple buildings were damaged, including an Aeon shopping centre that NHK said had suffered an explosion, while footage from the broadcaster also showed other buildings on fire or partially collapsed.
Large cracks appeared on major roads, including an elevated highway, and a goods train derailed, according to NHK, while rail services were halted and flights grounded.
TSMC, the world's largest contract chipmaker, evacuated workers from its plant in the area as a precaution, a spokesperson for the firm said.
Sony and Fujifilm also evacuated staff from their plants in the area, Nikkei newspaper reported.
More than 150,000 people have been instructed to go to evacuation centres, the disaster management agency said.
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.
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.
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.
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.
No irregularities were 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.
Some portions of the stone walls at the castle also collapsed as a result of Tuesday's quake, an official at the castle's office said.
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