No tsunami warning was issued and no damage was immediately reported.
The US Geological Survey (USGS) said the quake, which struck at 2.47pm local time (1547 AEST), had a magnitude of 6.0 and hit less than 11 kilometres below ground.
Japanese officials had put the magnitude at 6.3.
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Its epicentre was 70 kilometres south of Fukushima city in the prefecture of the same name.
The latest quake came as the severity rating of the nuclear disaster at Fukushima was raised to the same level as that of the Chernobyl disaster in 1986.
Emergency workers grappling to bring stricken reactors under control at the Fukushima Daiichi nuclear plant were ordered to evacuate, an official from operator Tokyo Electric Power said.
"We have no report of any abnormality in the external power to the Fukushima Daiichi plant. But we are inspecting the status of the water hosing and parameters in the area," the official said.
The quake was the second strong aftershock to strike the region on Tuesday, after a magnitude 6.2 offshore quake hit at 8.08am (0908 AEST).
That quake had a depth of 13.1km, with its epicentre 77km east of Tokyo, the USGS said.
It caused buildings to sway in the Japanese capital and temporarily stopped subway services.
Its magnitude was initially reported by the USGS as 6.4, while the Japan Meteorological Agency had measured it at 6.3.
Japan has experienced more than 400 major aftershocks stronger than 5.0 in magnitude since the 9.0 earthquake which unleashed a devastating tsunami on March 11.
Frayed nerves were strained further on Monday when coastal areas were put on alert for a possible tsunami after a 6.6 magnitude quake, which Jiji Press said was known to have killed at least one person.
