The powerful temblor followed a 6.5-magnitude earthquake that hit the Kyushu region late on Thursday and left nine people dead and over 1,000 people injured.
The quake triggered landslide in Minamiaso village, Xinhua news agency reported.
Houses in the Aso city collapsed and roads bulged after the quake. A main way in the city heading to Kumamoto city was blocked due to severe damages.
The Japanese government top spokesman, Yoshihide Suga, said around 20,000 Self-Defence Forces members were dispatched to the prefecture to help disaster relief operations.