The 6.2 magnitude quake struck Saturday night at a depth of 10 kilometres (six miles) in Nagano prefecture northwest of Tokyo.
A total of 41 people were injured, seven seriously, but no one was killed.
The quake also seriously damaged Nagano's famous Hakuba Village, a popular ski resort that hosted part of the 1998 Winter Olympics.
The Nagano prefectural government said more than 460 houses and other buildings were damaged while landslides hit at least four areas in the region.
"The government is determined to offer firm support, including rebuilding houses," he told reporters.
The meteorological agency has warned of possible strong aftershocks this week.
There was no damage to the seven nuclear reactors at the sprawling Kashiwazaki-Kariwa plant in neighbouring Niigata prefecture. They have been off-line since 2011.
Japan sits at the junction of several tectonic plates. Every year it is hit by around a fifth of the world's powerful quakes.
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