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
A handout photo made available by the United States Geological Survey shows the location of a 5.9 magnitude earthquake which struck at a depth of 8 km off the coast of the northern island of Hokkaido, at 107 km north east of Shibetsu, Japan, 05 November 2018. There were no official reports of damage or casualties. EPA-EFE/USGS / HANDOUT HANDOUT EDITORIAL USE ONLY/NO SALES