The Magnitude 6.7 quake struck 70 miles south of Sapporo on the island of Hokkaido, according to the US Geological Survey (USGS).
The tremor triggered a landslide which covered homes in the rural town of Atsumi trapping residents inside.
People in Sapporo were woken up by strong shaking shortly after 7pm BST (3am Thursday local time) as the earth moved for around 20 seconds.
Japanese TV showed damaged buildings and quoted police as saying some people had been trapped in collapsed structures.
Prime Minister Shinzo Abe said officials have set up a command center to coordinate rescue efforts.
At least 10 people have been taken to hospital after being injured in the quake.
Reports of power outages in Japan’s northernmost prefecture have been widely shared on social media.
One Twitter user said: “Just woke up to a pretty damn big earthquake in Sapporo. I’ve been through quite a few before and I’m shaking like a leaf right now. In fact, we’re getting an aftershock right now…”
The tremor struck at an approximate depth of 20 miles, USGS data said.
No tsunami warning has been issued following the earthquake, which was initially reported as a Magnitude 7.0.
The epicenter was just 16 miles from the city of Chitose, home to Hokkaido’s main airport.
A Twitter user named Licia said: “My friends. We just had a major #earthquake here in Japan. #Hokkaido. #Sapporo. We are in the dark, but otherwise fine. Omg! It was humongous. No information on magnitude. Internet still works for now.”
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