The 6.9-magnitude quake struck the region of Fukushima - the same area left devastated in 2011 when a 9.0-magnitude quake triggered a tsunami and a nuclear disaster which killed 18,000 people.
Thousands of people fled to higher ground after the tremors were felt.
There were fears that 3m high tsunami waves could hit the region after the early morning earthquake, but the highest wave measured 1.4m.
After the latest quake, the Tokyo Electric Power Company (TEPCO) said the cooling system for spent nuclear fuel at its Daini nuclear plant had been briefly halted.
No damage has been reported at the company's other plants, although there have been some blackouts, a spokeswoman said.
TV pictures showed ships moving out to sea as tsunami sirens wailed.
The quake struck off the Japanese coast, 67km northeast of Iwaki city, at a depth of 11.4km, the US Geological Survey (USGS) said.
An Iwaki fire department official said there was smoke or a fire at a petrochemical research centre, but that it had been extinguished.
Tokyo, 150 miles south, also felt tremors from the earthquake - which struck at 6am local time (9pm GMT).
There are so far no reports of serious damage or injuries.
The country's meteorological agency put the earthquake at 7.3 magnitude, but the reading by the USGS was later downgraded to 6.9.
Japanese broadcaster NHK said the East Japan Railway Company had suspended some of its bullet train services.
Japan accounts for 20% of the world's earthquakes greater than 6.0 magnitude.
The 2011 disaster in Fukushima was the world's worst nuclear disaster since Chernobyl and left more than 18,000 people dead or missing.
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