The quake hit at 2:42 pm (0542 GMT) at a depth of 10 kilometres (6 miles), according to the Japan Meteorological Agency.
Shinkansen bullet trains were suspended between Nagano and Kanazawa, a popular tourist site, according to Japan Railway.
The quake registered an upper six on the Japanese Shindo scale of up to seven in Suzu city, Ishikawa, meaning it could cause major landslides.
The US Geological Survey put the magnitude of the quake at 6.2.
Earthquakes are common in Japan, which sits on the Pacific "Ring of Fire", an arc of intense seismic activity that stretches through Southeast Asia and across the Pacific basin.
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