There was no risk of tsunami waves, the agency said.
The tremor hit at 7:20 am (2220 GMT Sunday) in northern Miyagi and Fukujima prefectures.
The quake was located in seas off Miyagi, roughly 350 kilometersmiles) northeast of Tokyo, at the depth of about 20 kilometers, the agency said.
Japan experiences 20 percent of the world's major earthquakes.