The epicenter of the earthquake was located off the eastern coast of the Pacific Ocean between the prefectures of Aomori on Honshu Island and Hokkaido at a depth of 20 kilometers (12.4 miles), according to the agency.
Tremors were felt across six prefectures.
The maximum seismic intensity of the earthquake was four on Japan's 7-grade scale. No tsunami warning was issued.
There have been no immediate reports of casualties or material damage.