The government Meteorological Agency warned people to stay away from the Pacific coast for nearly two hours as the tsunami, which was recorded as being as high as 55 centimetres (22 inches) in one place, rolled ashore.
Two workers who had been patrolling wells used to measure underground water at Fukushima sought higher ground after the tremors struck, an official with the plant's operator Tokyo Electric Power Co. (TEPCO) said while adding there were no new problems at the facility.
"There were few workers on the waterfront as it was night time. There was no impact of the quake and tsunami on the plant," he told local media.
Another nuclear plant, at Onagawa, was the site of the largest wave recorded on Saturday -- 55 centimetres -- but there were no problems reported there.
All of Japan's 50 viable reactors are currently shut down.
The 7.1-magnitude quake struck at a shallow depth of 10 kilometres (six miles) at 2:10am local time (1710 GMT Friday), just over 300 kilometres southeast of Ishinomaki in Miyagi Prefecture, according to the US Geological Survey.
The country's meteorological agency said the quake was an aftershock of the March 2011 tremor.
"We have lifted all tsunami alerts 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," Keiji Doi, director of the meteorological agency's quake predictions, told an early morning news conference.
"There is the possibility that aftershocks with a magnitude of around seven will occur once in a while."
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 3 am, while Ishinomaki, which was devastated in 2011, recorded a 30-centimetre wave.
"We evacuated as a matter of precaution because the ground floor of our house was flooded in the tsunami two years ago," Chimaki Hojyo, a 69-year-old housewife in Ofunato, told the Yomiuri newspaper. "This kind of tsunami will keep us worried."
Eastern Japan, a seismically active region, was struck by a 6.5 magnitude earthquake last month causing tremors that were felt 600 kilometres away in Tokyo.
The 2011 quake-tsunami knocked out cooling systems at the Fukushima nuclear plant, sending reactors into meltdown and forcing mass evacuations.
The effects of that disaster -- the world's worst nuclear accident since Chernobyl 25 years earlier -- are still being felt.
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.
TEPCO's own estimates suggest the full decommissioning of the site could take up to four decades and that much of the trickier work is yet to be done -- notably the removal of reactor cores that have probably melted beyond recognition.
According to the utility's own plan, these reactor cores -- which are feared to have seeped into the containment vessels and possibly even eaten through thick concrete -- will be removed around 2020.
Although TEPCO says the reactors are now under control, critics say the plant remains in a precarious state and at the mercy of extreme weather or further earthquakes. They point out that there is still no plan for the thousands of tonnes of water being stored on site.
Tens of thousands of people remain in temporary accommodation, with some scientists warning that it could be decades before they are able to return home -- if at all.