The 5.3 tremor struck the region of Akita, in the north west of the counrty.
According to the Japan Meteorological Agency (JMA), the earthquake took place 10 kilometres beneath the surface at around 10.20PM local time.
According to local media outlet NHK, there have been no reports of damages to buildings.
In addition, the JMA has said: “This earthquake poses no tsunami risk.”
The tremor in Japan comes just hours after a huge earthquake hit Mexico, claiming the lives of at least 32 people.
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The 8.2 quake struck 60 miles off the southern coast of Mexico, sparking tsunami warnings.
In Juchitan in Oaxaca state, parts of the town hall, as well as numerous other structure, have been reduced to rubble while the quake caused damage to homes and buildings across southern part of the country.
More than 50 million people felt the enormous quake as buildings shook in Mexico City and tremors were also felt in neighbouring Guatemala and the US state of Texas.
Both Japan and Mexico are situated on the deadly Ring of Fire – a huge 40,000 kilometre stretch where several fault lines connect and is often associated with heightened seismic activity.
Explaining the Ring of Fire, University of Technology Sydney’s Dr Behzad Fatahi, a lecturer in Earthquake Engineering, has said: “The borders of a lot of tectonic plates meet in the Ring of Fire, they move away from each other and push each other, it’s one of those very active areas.”