There was no damage to property and loss of life reported and no tsunami warning has been issued.
The Japan Meteorological Agency earlier reported it at 5.6 magnitude.
Both runways at Narita International Airport in Tokya were closed for staff to inspect for any damage. Neither was found to have been affected.
The epicenter was located in the northern part of Saitama Prefecture, north of Tokyo, Japan Times reported citing NHK.
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Japan is located at the junction of a number of the earth's tectonic plates and experiences around a fifth of the planet's most powerful quakes every year. Rigid building codes and strict enforcement mean that even powerful quakes frequently do little damage to infrastructure.