By Agence France-Presse
The quake was at a depth of 10 kilometres (6 miles) about 30 kilometres west of Ina in Nagano prefecture at 7:02 am (2202 GMT on Saturday), the US Geological Survey said.
There were no immediate reports of injuries or damage, according to public broadcaster NHK. The Japan Meteorological Agency did not issue a tsunami warning.
Shinkansen bullet train services were temporarily suspended due to the jolt in central Japan, while no abnormality was reported at nuclear power plants in the region, NHK said.
Japan sits at the junction of four tectonic plates and experiences a number of relatively violent quakes every year. But rigid building codes and strict enforcement mean even strong tremors often do little damage.
A massive undersea quake that hit in March 2011 sent a tsunami barrelling into Japan's northeast coast, leaving more than 18,000 people dead or missing, and sending three reactors into meltdown at the Fukushima nuclear plant.