Japanese broadcaster NHK said a number of calls were coming in from residents reporting people being trapped inside houses and buildings.
The quake shook the Kumamoto region at 1.25am local time, and several aftershocks soon followed.
Japan’s Meteorological Agency issued an advisory for a tsunami up to 1m high along the coast west of the epicentre in Kumamoto; the advisory was lifted less than an hour later.
Sirens of patrol vehicles were heard in the background as NHK reported from the hardest-hit town of Mashiki. The asphalt ground outside the town hall had a new crack, apparently made by the latest earthquake.
The Nuclear Regulation Authority said no abnormalities were found at the Sendai nuclear plant, where the only two of Japan’s 43 reactors still operable are situated.
Thursday’s weaker, magnitude 6.5 earthquake brought down buildings and injured about 800 people, in addition to the nine deaths.
The epicentre of yesterday’s earthquake was about 12km north-west of Thursday’s, and at a depth of about 10km, yesterday’s quake was more shallow.
It hit residents who were still in shock from the previous night’s horrors and had suffered more than 100 aftershocks in the interim.
A bright spot, broadcast repeatedly on television yesterday was the overnight rescue of an apparently uninjured baby, wrapped in a blanket and carried out of the rubble of a collapsed home.
About 44,000 people stayed in shelters after Thursday’s quake.
The dead included five women and four men, the Fire and Disaster Management Agency said. One man was in his 20s, and the rest of the victims ranged from their 50s to one woman in her 90s. Eight of the nine victims were from Mashiki.
There were varying reports on the number of injured. The government’s chief spokesman, Yoshihide Suga, said at least 860 people had been injured, 53 seriously. Kumamoto prefecture tallied 784 injured.
Most of Japan’s nuclear reactors remain offline following the meltdowns at the Fukushima plant in 2011 after a magnitude 9.0 earthquake triggered a huge tsunami.
According to the Japan Meteorological Agency, Mashiki sits near two faults on Kyushu. The area is also near Mount Aso, a huge, active volcano. JMA officials said the quake was unusually strong for Kyushu.