Xinhua reporters in Mashiki have been feeling aftershocks hitting regularly and there was widespread panic in the town with people seen flee from buildings to open areas, with some ducking into vehicles for protection.
The town being plunged into darkness following a power cut is adding to the alarm.
The latest quake, following hundreds of aftershocks in the wake of quakes striking overnight a day earlier and claiming the lives of nine people and injuring more than 1,000, in Kumamoto, measured in the upper six range of Japan's seismic scale which peaks at 7, the JMA said.
The quake struck at a latitude of 32.8 degrees north and longitude of 130.8 degrees east.
As with the previous major quake, the epicenter was relatively shallow at a depth of just 10 km.
The number of fatalities and injuries, as yet, has been unreported by prefectural officials and rescue services in the quake-hit region.
Chinese diplomats have been assigned to the quake-affected areas, seeing students from China.
Whether or not Prime Minister Shinzo Abe's planned trip to the already quake-ravaged region, scheduled for Saturday, will go ahead as planned, has yet to be confirmed by his office.
Following the latest quake, large sections along major arterial routes and expressways have been closed off, the traffic information center said.