Officials say the aftershock hit at about 11:30 p.m. Thursday Japan time. The quake had a preliminary magnitude of 7.4, but it was later downgraded.
It hasn't been a month since much of Japan was devastated by an earthquake and tsunami, which then caused a partial meltdown at damaged nuclear power plants. Now, the strong aftershock and another tsunami warning sent people fleeing to higher ground.
The expected time for tsunami came and went, and the warning was lifted. So far, there are no reports of serious injuries.
"I think they are taking no chances after what happened, but generally a big tsunami takes a quake that is usually in the (magnitude) eights, and usually in the upper eights," Caltech seismologist Kate Hutton said.
There was moderate damage reported in buildings where water came through the roof. Electric power was out in many cities.
The aftershock hit 25 miles under the water off the coast of Miyagi prefecture. Shallower quakes tend to be more destructive.
The quake that preceded last month's tsunami was a 9.0-magnitude. Hundreds of aftershocks have shaken the northeast region devastated by the March 11 earthquake, but few have been stronger than 7.0.
Buildings as far away as Tokyo shook for about a minute.
There were no immediate reports of damage at the Fukushima reactors after the strong aftershock.
Attempts to cool the reactors has continued but has been interrupted by the aftershock. The aftershock knocked out electric power at a couple of reactors, but NHK television reported that backup power worked as planned.
Paul Caruso from the USGS said the quake hit at about the same location and depth as the March 11 quake. Except for a 7.9 aftershock felt that same day, Thursday's was the strongest of more than 1,000 aftershocks.
The Associated Press contributed to this report.