No immediate casualties or damage were reported.
The quake occurred at 1322pm local time (1722 AEDT), with its epicentre off Ibaraki prefecture, the agency said.
No new damage or abnormalities were reported at the damaged Fukushima Daiichi Nuclear Power Station.
The north-eastern region was hit by a magnitude-9.0 quake and tsunami on March 11. The disaster left more than 15,000 dead and nearly 3300 missing.