The epicentre of the first quake, with a magnitude measuring 5.7, was located some 91 kilometres (56 miles) off the coast of Honshu, Japan's largest and most populated island, at a depth of 22 kilometres shortly after 3:00am local time (2330 IST Sunday).
A second, 5.6-magnitude quake struck two hours later slightly closer to shore at a depth of 39 kilometres.
Cities nearest to the epicentre included Iwaki, Kitaibaraki, Namie and Hitachi, USGS said.
The Japan Meteorological Agency put the magnitude of the first quake today slightly higher at 5.8, adding that there was no immediate risk of a tsunami.
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Japan is situated at the conjuncture of several tectonic plates and experiences a number of relatively violent quakes every year.
But thanks to strict building codes, even powerful quakes that might wreak havoc in other countries frequently pass without causing much damage.