The earthquake injured 125 people on the island of Hokkaido after it hit yesterday and caused landslides that covered houses and left people trapped.
The first shock was measured 6.7 on the Richter scale, which measures the magnitude, near the city of Sapporo.
One of the people that died was an 82-year old man, who fell down his stairs during the earthquake, local government officials reported.
The natural disaster also led to widespread blackouts, after Hokkaido Electric Power Company said it conducted an emergency shutdown of all its fossil-fuel-fired power plants.
The entire island and its 5.3million residents have been left without power and a company spokesman said it wasn’t clear when electricity would be restored.
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A nuclear power plant also lost power, but was cooling its fuel rods safely with emergency power, according to chief cabinet secretary Yoshihide Suga.
He added the operator reported no radiation irregularities.
A fire broke out at a Mitsubishi Steel Mfg Co plant in the city of Muroran after the quake but was mostly extinguished with no injuries, a company official revealed.
Aerial footage reveals dozens of landslides occurred near the town of Atsumi, a rural town in southern Hokkaido, with mounds of reddish earth and fallen trees piled up at the edge of green fields, alongside what appears to be the collapsed remains of houses or barns.
Bits of roof and water could be seen on the floor in New Chitose Airport, which is likely to be closed at least for today, affecting more than 200 flights and 40,000 passengers.
The quake, which hit at 3.08am local time (6.08pm yesterday GMT), posed no tsunami risk according to the Japan Meterological Agency.
It was followed up by a fresh quake which hit 29km east of the coastal city of Tomakomai, measured at 5.4 on the Richter scale.
Prime minister Shinzo Abe said the government has set up a command centre to coordinate relief and rescue, with 25,000 troops dispatched to the area.
He said saving lives was his government’s top priority.
Japan is situated on the “Ring of Fire” where two tectonic plates join and accounts for 20 percent of the world’s earthquakes magnitude 6 or greater.
The earthquake came just days after Japan suffered it’s seventh Typhoon this year, the strongest in 25 years.