The quake caused the metropolitan area of the city to shake – leaving residents on high alert. The epicentre of the earthquake was just outside of Chiba-shi in Japan, 52km east of the capital city.
No tsunami warnings are currently in place.
The earthquake had a depth of 80 kilometres (48 miles).
A number of eyewitness reports have since come in following the earthquake.
One report reads: “Strong shake. Vibration first with up and down motion. Then left to right swaying. Enormous and quite lasted a minute.”
The effects of the earthquake were also felt near Tokyo Bay.
One eyewitness report reads: “Strong shaking near north part of Tokyo Bay.”
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The earthquake hit Hashikami, Aomori Prefecture, at around 2:46 a.m on Wednesday.
The earthquake reached upper 5 on the Japanese seismic intensity scale of 7.
According to the JMA, the earthquake had a depth of 56 kilometres, with the epicentre in the Pacific Ocean off the coast of Iwate Prefecture.
The meteorological agency had originally recorded a magnitude of 6.0 in the scale, but subsequently corrected it to 5.9, as well as changing the focal depth from 50 km to 56 km.
A liaison office in the prime minister’s office was set up to try and understand what consequences they would face following the impact of the quake.