The 5.4 magnitude jolt was felt in Tokyo and areas of eastern Japan at 11:47 am, the US Geological Survey said.
The quake comes a week after the capital's high-rise buildings were shaken by a 5.0 quake.
Quakes of a similar scale also shock Tokyo on July 17 and 19.
The epicentre of today's quake was east of the capital in Ibaraki prefecture at a depth of about 46.7 kilometres, the USGS said.
There was no threat of a tsunami, the Japan Meteorological Agency said.
A massive undersea quake that hit in March 2011 sent a tsunami barrelling into Japan's northeast coast, leaving more than 18,000 people dead or missing, and sending three reactors into meltdown at the Fukushima nuclear plant.
In April, two strong earthquakes hit southern Japan's Kumamoto prefecture followed by more than 1,700 aftershocks, and left 49 dead and caused widespread damage.
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