The agency did not issue a tsunami warning.
The epicentre of the 12:06 pm (0306 GMT) quake was around the Russian-administered Kurile Islands, east of the northern island of Hokkaido, at a depth of 10 kilometres, the agency said.
A series of quakes has struck across Japan in recent days. On Saturday, a magnitude-6.3 quake shook Awaji Island, western Japan. Thirty-two people were injured and 2,886 houses were damaged by the quake, the Kyodo News agency reported.
A government committee said 390 aftershocks were recorded in the region in the 25 hours since the main quake.
On Wednesday, a magnitude-6.2 quake jolted Miyake Island, 180 kilometres south of Tokyo, injuring at least three people, according to local media. There were around 40 tremors on the islands on that day alone, the agency said.//DPA