Multiple, large-scale landslides struck the sparsely populated countryside, which was also hit by the edge of a powerful typhoon that surged through Japan earlier this week, Channel NewsAsia reported.
Aerial views showed dozens of houses destroyed at the bottom of a hill, with a rescue helicopter winching a resident to safety.
Around 3 million homes lost power after the quake damaged a major thermal plant supplying the region.
The Tomari nuclear power plant in Hokkaido, which was not operational before the quake, was forced to turn to emergency backup power to keep its cooling system working, NHK said.
Kazuo Kibayashi, a town official at hard-hit Abira town, told AFP: "There was a sudden, extreme jolt. I felt it went sideways, not up-and-down, for about two to three minutes."
"It stopped before shaking started again. I felt it come in two waves. I am 51, and I have never experienced anything like this. I thought my house was going to collapse. Everything inside my house was all jumbled up. I didn't have time to even start cleaning," he added.
Around 20,000 rescue workers, including police and members of the Self-Defence Forces were responding to the disaster, government spokesman Yoshihide Suga said. Another 20,000 SDF troops are expected to join the effort.
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