Japan's Meteorological Agency (JMA) lifted the tsunami warning at 02:14 local time, following the strong earthquake which hit the southwest once more within a day.
The agency said more aftershocks are expected as well as possible landslides and buildings collapsing, as inclement weather is expected overnight and through the weekend.
Kumamoto Prefecture in southwestern Japan was rocked again by a magnitude-7.2 earthquake on Saturday at 01:25 local time, with the temblor being felt across wide swathes of southern Japan and triggering a tsunami warning, although the advisory was soon lifted.
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 kilometers.
According to Xinhua reporters in the vicinity of the quake, after shocks could still be felt as of 02:10 a.m. local time.
Travellers told Xinhua's reporters in Aso, some 30 km off the epicenter, that the tremor they felt recalls the 1995 massive earthquake, which claimed around 6,500 lives.
The reporters have been witnessing more aftershocks.
