Japan's meteorological agency denied the possibility of a tsunami following the 5.0 magnitude earthquake
Tokyo was struck by a third earthquake in four days on Wednesday, but there were no reports of damage or casualties.
The 5.0 magnitude jolt was felt in Tokyo and areas of eastern Japan at 7:25 am (2225 GMT Tuesday), the US Geological Survey said.
It was the third quake to shake the capital's high-rise buildings in recent days, following a 4.8 magnitude quake on Tuesday and one of 5.0 on Sunday, but an official with the Japan Meteorological Agency said they weren't a precursor of a major jolt.
"This is an area that sees frequent earthquakes" of a moderate size, Nariaki Ohkawara told AFP, adding that the latest quakes were part of that trend.
The epicentre of Wednesday's quake was east of the capital in Ibaraki prefecture at a depth of about 44 kilometres (27 miles), the USGS said.
There was no threat of a tsunami, the Japan Meteorological Agency said.
Japan sits at the junction of four tectonic plates and experiences a number of relatively violent quakes every year, but rigid building codes and strict enforcement mean even powerful tremors frequently do little damage.
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.
The country routinely holds emergency drills to prepare for a major jolt, and the government stepped up its disaster response in the wake of the 2011 devastation.