A shallow magnitude 6.0 earthquake struck off the northern coast, 167 kilometres (103 miles) from Miyako city, the US Geological Survey said.
There was no threat of a tsunami following the quake which had a depth of 10 kilometres, the Japan Meteorological Agency said.
The jolt came one day after a 5.3 magnitude earthquake struck northeastern Japan off the coast of Ibaraki prefecture, just south of Fukushima.
The crippled Fukushima Daiichi nuclear power plant, battered by a massive 2011 earthquake-generated tsunami and which is currently being decommissioned, has shown no irregularities in radiation levels following Friday's jolt, officials said.
Japan sits at the junction of four tectonic plates and experiences a number of relatively violent quakes every year, but rigid building codes and their strict enforcement mean even strong tremors often do little damage.
But the massive undersea quake that hit in March 2011 sent a tsunami barreling into Japan's northeast coast, leaving more than 18,000 people dead or missing, and sending three reactors into meltdown at the Fukushima nuclear plant.
In April, two strong earthquakes hit southern Japan's Kumamoto prefecture followed by more than 1,700 aftershocks, leaving 50 dead and causing widespread damage.
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