Seismologists said the epicentre was around 44 kilometres north-northeast of the Japanese capital and was located around 50 kilometres (30 miles) below the surface.
The US Geological Survey said the quake had a magnitude of 5.6. Their Japanese counterparts said there was no danger of a tsunami from the tremor, the effects of which could be felt in buildings for more than a minute after the initial shaking began.
The operator of the Fukushima nuclear plant, which was battered by a tsunami after a powerful undersea quake in 2011, said nothing unusual had been noted at the still-fragile site.
"There was no abnormality in our monitoring at the Fukushima Daiichi nuclear power plant following the earthquake. Also, we have not received any reports of damage from the latest quake," spokesman Keisuke Murakami said.
The Japan Atomic Power Co. said the Tokai No.2 Power Station, which was nearest to the epicentre of the quake, showed no signs of any problems.
An official at the Ibaraki prefectural government said checks were ongoing, but that so far there appeared to be nothing amiss in the wider area.
"We have not received any reports of damage, injuries or casualties following the earthquake. We are still checking if the quake could result in damage," he said.
Japan is hit by around a fifth of the world's powerful quakes every year and sits at the conjunction of several tectonic plates.
Building codes are rigorous and regular disaster drills are held, helping to ensure that despite their frequency and their violence, quakes usually pass without loss of life or significant damage to property in Japan.
However, the 9.0 magnitude undersea quake of March 2011 sparked a huge tsunami that smashed into the country's northeast coast, killing around 18,000 people and creating the world's worst nuclear emergency in a generation.