The fresh earthquake hit 29km east of Tomakomai, a coastal city on Hokkaido.
The aftershock measured 5.4 on the Richter scale.
According to US earthquake specialist Charles Richter this is likely to have caused: “Damage of varying severity to poorly constructed buildings.
The tremor would have been “felt by everyone”.
It comes shortly after the city of Sapporo, also on the island of Hokkaido, was hit by a calamitous 6.7 magnitude earthquake.
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This caused a landslide which buried homes in the rural town of Atsumi, trapping residents inside.
Local government officials are reporting that an 82-year-old man has died after falling down the stairs in his home during the earthquake.
Another 10 people were taken to hospital with injuries.
Several parts of Hokkaido Island remain without power.
According to the US Geological Survey the 6.7 magnitude earthquake struck 112km southeast of Sapporo, a major city.
Japanese Prime Minister Shinzo Abe said a command centre had been setup to coordinate the response.
Japan is located in the so-called ‘Ring of Fire’, an area bordered by oceanic trenches and volcanoes which is particularly susceptible to earthquakes.
About 20 percent of the world’s earthquakes which reach magnitude 6 or greater occur in this region.
Japan is still recovering from a devastating typhoon which hit western parts of the country on Tuesday.
The freak weather left 11 dead and trapped thousands of passengers at Kansai international airport, after the bridge linking the island airport to the mainland was damaged by a tanker.