Across the prefecture, which also suffered a deadly earthquake a decade ago, around 260,000 people were instructed to go to evacuation centres, authorities said.
The quake’s epicentre was about 20 kilometres (12 miles) south of Kumamoto City, central Kyushu's largest city with a population of around 700,000.
Authorities have warned residents in the areas that felt the biggest tremors to be on alert for further strong quakes for about a week, as well as for the risk of landslides.
With more than 36,000 homes still without power, authorities are worried about the risk of heat stroke as temperatures soar to around 34 degrees Celsius (93 degrees Fahrenheit) on Wednesday.
SOME HOSPITALS OVERSTRETCHED
One hospital in Uki city, near the epicentre, said a power outage caused by the earthquake meant it was unable to function.
"It's become like a field hospital," the head of the administrative department told NHK. Another hospital in the city said it had suspended admissions as it could no longer handle additional emergency cases after accepting 86 injured people following the quake, including three with serious injuries.
Several passengers aboard high-speed trains at the time of the quake were also injured, operators said.
But it was the Aeon mall (8267.T), opens new tab, the largest in the prefecture, that was the most eye-catching disaster.
One side of the mall, which houses around 200 stores, was torn away in the blast, exposing steel beams and strewing debris across a parking lot, footage showed.
A spokesperson for mall operator Aeon 8267.T said customers and employees were evacuated right after the initial quake and that the exact cause of the ensuing explosion was unclear.
Aeon shares fell 1.9% in early trading in Tokyo. The benchmark index (.N225), opens new tab was up 0.8%.
Some major companies with plants in the area including Tokyo Electron (8035.T), opens new tab, a semiconductor equipment maker, and Honda (7267.T), opens new tab said they would suspend operations at their plants through Wednesday.
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TSMC (2330.TW), opens new tab, the world's largest contract chipmaker, evacuated workers from its local plant as a precaution after the quake but said it had begun resuming operations late on Tuesday.
Some roads were also badly damaged, with large cracks splintering major highways and snarling traffic on Tuesday evening.
Located on the "Ring of Fire" of volcanoes and oceanic trenches partly encircling the Pacific Basin, Japan accounts for about 20% of the world's earthquakes of magnitude 6.0 or more.
A massive earthquake in Kumamoto 10 years ago killed 275 people and injured a further 2,739, according to an official count, and damaged thousands of buildings including the walls of the city's castle, a top tourist site.
