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The earthquake occurred about 5.30am local time, according to reports from the Japan Meteorological Agency, which monitors seismic activity.
The earthquake's epicentre was roughly 25 miles off the coast of Japan, it suggested, adding that there was no threat of a tsunami.
Mild rumbling at the Games was reported by journalists in Tokyo, with reports saying it lasted between 20 seconds and three minutes.
Australian journalist Mark Beretta, who was in the middle of a live broadcast from on top of a temporary broadcast tower, told viewers the roof above him was moving.
He said: “Welcome back to the Olympic city where we are currently in an earthquake, an earth tremor.
“The roof above us is moving and you might notice our lights and camera are moving as well.
“That was quite an unusual moment, I have not been through an earthquake before.”
Japan is a country which rests on three converging tectonic plates, with earthquakes occurring when just one of them shifts.
The Olympic Games venues were created to withstand earthquakes and other natural disasters.
For example, the Ariake volleyball arena contains “shock-absorbing giant rubber cushions”, while the Olympic Village is protected by sea walls that can protect against tsunamis reaching 6.5 feet.
“For organisers, infection measures are an urgent challenge,” Hirotada Hirose, a Japanese specialist in disaster risk studies, told AFP.
“But the risks of a major earthquake mustn’t be forgotten when you have an Olympics hosted by Japan.”
An earthquake in 2011 triggered a tsunami that killed around 18,500 people and caused the Fukushima nuclear disaster.