The moderate quake hit at a depth of eight kilometres (five miles), 107 kilometres northeast of Shibetsu.
USGS said there was a low likelihood of casualties and damage.
It comes after a powerful 6.6-magnitude quake in September rocked Hokkaido, triggering landslides, collapsing houses and killing more than 40.
Japan sits at the junction of four tectonic plates and experiences a number of relatively violent quakes every year.
But rigid building codes and strict enforcement mean even strong tremors often do little damage. DM
This article is more than 7 years old
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5.9-magnitude earthquake strikes off Japan's Hokkaido: USGS
A shallow 5.9-magnitude earthquake struck off Japan's northern island of Hokkaido on Monday, the US Geological Survey said.
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