There was no risk of tsunami waves, the agency said.
The epicenter of the quake, which took place at 3:32 am (1832 GMT Friday), was located in seas off the east coast of Honshu, about 375 kilometersmiles) northeast of the capital Tokyo, the US Geological Survey reported.
The quake occurred at a depth of 50 kilometers, according to both Japanese and US seismologists.
The US Geological Survey estimated the magnitude of the quake at 5.9.
Japan experiences 20 percent of the world's major earthquakes.