A quake hit Kumamoto prefecture of the southwestern island of Kyushu at 1.25am (1625 GMT Friday) according to US Geological Survey.
The magnitude of 7 has been revised to 7.3 according to source.
The quake left the entire city of 730,000 without power.
Residents and guests were evacuated as the powerful shaking sent some buildings partially collapsed.
“The latest earthquake felt as strong as, or stronger than the original one,” Sakamoto, told AFP. “It was really strong … Many people on the street appeared panicked.”
At least 2 people were killed in Japan’s magnitude 6.2 quake, officials say. https://t.co/PUOZ9fSHbB
— CNN Breaking News (@cnnbrk) April 14, 2016