The epicentre, at a depth of 10 km, was near Hamadori in Fukushima prefecture.
The impact was felt as far away as Tokyo, 200 km to the south, where skyscrapers swayed in the aftershocks.
Two-metre-high tsunami waves were expected to hit the Pacific coast in Ibaraki prefecture, the agency said, urging people to evacuate to higher locations.
Nuclear power stations in Ibaraki were normal after the quake, officials said.
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