The tremor occurred 83 kilometers (51 miles) east of Minami-Soma in the province of Fukushima at a depth of 40 kilometers, the agency said, with no tsunami warning issued.
There was no report of any damage.
According to Japanese media, the quake was felt in Iwate, Miyagi, and Fukushima provinces at 12.16 p.m. local time (0316GMT), with no abnormalities confirmed at the crippled Fukushima Daiichi nuclear power plant.
This came after a powerful magnitude 7.4 earthquake struck off Taiwan's eastern coast on Wednesday, killing at least nine people, while hundreds others were injured.
The quake was the strongest to have hit the island nation in 25 years. In 1999, around 2,400 people were killed when a 7.7-magnitude earthquake struck Taiwan in the middle of the night.
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