The U.S. Geological Survey said the quake measured 6.3, which led meteorologists to issue a tsunami warning.
CNN said the Japanese Meteorological Agency had issued tsunami advisories for Miyagi and Fukushima prefectures after the quake off Honshu, Japan's northeastern main island where Tokyo is located.
The warning was lifted after about 40 minutes, The Mainichi Daily News reported.
The USGS said the quake, at 1:36 a.m. EDT, struck at a depth of 24.3 miles near the east coast of Honshu, 61 miles southeast of Sendai and 175 miles northeast of Tokyo.
A 9-magnitude March 11 earthquake in the same region was followed by a monstrous tsunami that devastated vast areas, killed or left missing thousands of people, inflicted economic damage on Japan running into the multibillions of dollars and triggered a radiation-emitting Fukushima Daiichi nuclear plant crisis, which is yet to be fully resolved.
The Tokyo Electric Power Co., operator of the Fukushima plant, said no new abnormalities had been observed in the plant following the latest earthquake.