While it was not immediately clear whether the latest quake increased the death toll, authorities said hundreds of calls had come in from residents reporting people trapped inside houses and buildings.
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Residents living near a dam were told to leave because of fears it might crumble, broadcaster NHK said.
Widespread reports have emerged of multiple collapsed buildings and people trapped inside.
Mashiki, a town with the population of about 35,000 people, is near the quake’s epicentre.
The quake struck 11 km (7 miles) east of the city of Kumamoto, the U.S. Geological Survey reported. The entire city of 730,000 was without power.
More than 3,000 troops, police and firemen were dispatched to the area from around Japan, and Prime Minister Shinzo Abe said more would be sent if needed. “The buildings that were damaged in the original shock have now been redamaged or reshaken”, he said.
The magnitude 6.5 natural disaster registered the highest level of intensity on the Japanese seismic scale.
Tokohu University professor Shinji Toda added: “Thursday’s quake might have been a foreshock of this one”.
Gen Aoki, director of the Japan Meteorological Agency’s quake division, warned more aftershocks could occur over the next week. “Many people on the street appeared panicked”.
At 1:25 a.m. Saturday morning, the second quake with a preliminary magnitude of 7.1, hit the Kumamoto region.
NHK said the advisory suggested a possible wave of one meter in height. The advisory was lifted less than an hour later.
Chief Cabinet Secretary Yoshihide Suga said the damage was still being assessed but several homes collapsed.
It caused catastrophic meltdowns at the Fukushima Daiichi nuclear power plant.
By early Friday, 44,400 people have already been evacuated from their homes, filing 500 shelters in the prefecture.
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Japan, positioned along what’s known as the Pacific Ring of Fire, is no stranger to earthquakes but activity in Kyushu has kicked up in recent days.
