An earthquake of magnitude 7.3 struck early on Saturday morning off Japan's east coast, triggering a small tsunami, the US Geological Survey said.
The quake struck at a depth of 10km at 2:10am local time (1710 GMT) about 327km off southeast of Ishinomaki in Miyagi Prefecture.
As it stood down its warnings, Japan's meteorological agency said the quake was an aftershock of the March 2011 tremor.
"We have lifted all tsunami alert but the sea level may continue to show small changes for half a day or so please be very careful when working by the sea," an official told a press conference.
A spokesman at Tokyo Electric Power Co (TEPCO), operator of Fukushima, said there was no damage or spike in radiation levels at the station.
People were warned to stay away from the coast as the tsunami, which was recorded as being as high as 55 centimetres in one place, rolled ashore.
There were no reported problems at any other nuclear plant, including at Onagawa, the site of the largest wave - 55 centimetres - recorded Saturday.
All of Japan's 50 viable reactors are shut down.
Buildings shook as far away as Tokyo, 230km south of the nuclear plant.
The area affected largely overlapped with that hit by the March 2011 disaster when more than 18,000 people died after a towering tsunami crashed ashore following a 9.0 magnitude undersea quake.
In the town of Ofunato, a 20-centimetre tsunami was logged just after 3am, while Ishinomaki, which was devastated in 2011, recorded a 30-centimetre wave.
Ships were seen leaving a port south of the Fukushima Daiichi nuclear power station, where three reactors had meltdowns in 2011 after an earthquake and tsunami knocked out cooling and power, as a precaution after the tremor.
TEPCO is battling to clean up the mess at the plant where thousands of tonnes of radiation-contaminated water are being stored in tanks after being used to cool the reactors.
Frequent mishaps, including leaks of radiation-contaminated water and a power outage caused by a rat have shaken public confidence in the huge utility.
The Japan Meteorological Agency had issued a "yellow" warning shortly after the quake. The US Pacific Tsunami Warning Center however, did not post warnings for the rest of the Pacific.
The USGS initially said its magnitude was 7.5.