The quake struck at 10:08 pm (1308 GMT), with its epicentre at a depth of 10 kilometres (six miles) in the north of Nagano Prefecture, northwest of Tokyo, according to USGS and Japan Meteorological Agency, which measured it at 6.8.
There were no immediate reports of casualties or major damage, although some traffic was disrupted with the road and train authorities checking safety, public broadcaster NHK said.
There was no damage to any of the seven nuclear reactors at the sprawling Kashiwazaki-Kariwa plant in neighbouring Niigata prefecture as they have been off-line since 2011, NHK quoted the operator, Tokyo Electric Power Co., as saying.
Japan is hit by around a fifth of the world's powerful quakes every year and sits at the conjunction of several tectonic plates. A strong tremor revives memories of the 9.0 earthquake in March 2011, which triggered a tsunami which sparked the Fukushima atomic disaster and left some 18,000 people dead or missing.