At least 37 homes were destroyed in two villages, and 39 people were injured across the region, including seven seriously, mostly with broken bones, officials said.
The magnitude-6.7 earthquake struck shortly after 10pm local time yesterday west of Nagano city at a depth of 10 kilometres, the Japan Meteorological Agency said.
The agency revised the magnitude from a preliminary 6.8 while the US Geological Survey measured it at 6.2. Since the quake occurred inland, there was no possibility of a tsunami.
He said he was in the restaurant's wine cellar when the quake struck, and that nothing broke there.
Japan's Nuclear Regulation Authority said no abnormalities were reported at three nuclear power plants in the affected areas.
All of Japan's nuclear plants are offline following a magnitude-9.0 earthquake and massive tsunami in 2011 that sent three reactors at the Fukushima Dai-ichi plant into meltdown.
Fukushima is about 250 kilometres northeast of where yesterday's earthquake occurred.
Another seven homes were lost in Otari, a nearby village to the north. Non-residential buildings were also destroyed, with officials still assessing the extent.
Japanese television footage showed buildings in various states of collapse, some flattened and others leaning to one side, and deep cracks in the roads. A landslide spilled onto a railroad track, forcing service to stop. About 200 people have evacuated to shelters, almost all from Hakuba and Otari.
All 21 people trapped under collapsed houses were rescued, with two of them injured, the National Police Agency told Japan's Kyodo news agency.
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