The quake hit at 10:03 am (0103 GMT) in Ibaraki prefecture, 160 kilometers (100 miles) northeast of Tokyo, and some 80 kilometers southwest of the crippled Fukushima nuclear plant, according to Japan Meteorological Agency.
The tremor was 10 kilometers deep, the agency said, and was followed eight minutes later by a very shallow 3.6-magnitude quake in the same area.
The initial quake was strong enough to gently rock high-rise buildings in the capital.
Tokyo Electric Power said the quakes did not affect the Fukushima Daiichi nuclear plant, where crews are working through the holiday season to cool reactors crippled by the 2011 tsunami.