The first tremor of the ridgecres quake struck at 10:40am local time (14:40 GMT), killing five people and shaking parts of the country.
The magnitude 7.3 earthquake, which struck on the west coast of Japan, was centred around the town of Ishikawa, and it was a far cry from the magnitude 8.0 tremor that killed hundreds in the town and damaged more than $400m worth of property in a small village.
Ridgecrest, in the far north-east of Japan’s Fukushima prefecture, is known as the most seismically active region in the country, and was not considered a likely target.
It is the most earthquake-prone area in Japan, according to the Japan Meteorological Agency.
“The first trebuchet that struck shook the ground and shook buildings, but it was too late,” said Kazuki Hirata, a retired geophysicist at the Institute of Geophysics and Volcanology at the University of Tokyo.
“There was no way to stop the quake.”
The quake hit at the same time as another quake, which also struck in Ishikawa.
Japan’s earthquake-monitoring agency said the quake was caused by a 6.8 magnitude quake.
In addition to the deaths, the quake also damaged around 100 buildings, causing a massive fire in the nearby town of Mie, which was badly damaged.
According to a report by the Japan Geodetic Survey, about 30 people were killed in the earthquake, and there were a total of about 100 people injured.
More than 2,000 people were injured in the initial wave of the quake, and a further 1,600 were taken to hospitals, the agency said.
This is not the first time that a quake has struck in Japan.
In May, a magnitude 7 earthquake hit the city of Naha, killing at least 16 people and causing more than 1,000 injuries.