The quake struck at 10:08 pm local time (1308 GMT) at a depth of 10 kilometres (six miles) at the epicentre, in the north of Nagano Prefecture, northwest of Tokyo, according to USGS.
Television footage showed flattened wooden houses, a mudslide blocking a road and books fallen off shelves.
The Japan Meteorological Agency measured the quake at magnitude 6.8.
"It's quite a strong earthquake for an inland one," an official at the Japanese agency told a midnight press conference.
"We are worried about the extent of damage to houses and buildings," he said, adding that residents should also be on alert for possible landslides as mountainous areas were the hardest hit.
The quake toppled at least three houses in Hakuba Village, Nagano Prefecture, local police said, injuring one resident. No further details were immediately confirmed.
Public broadcaster NHK said 15 residents were temporarily trapped under the houses but all of them, including the injured person and a two-year-old toddler, were rescued.
Electricity was cut off at around 1,600 households.
Nagano police said several people sustained minor injuries in the quake.
But police and municipal officials said they were still scrambling to collect information as they were operating in the dark.
Yoshihide Suga, the top spokesman for the central government, told reporters that Tokyo was doing its best to get hold of the overall damage.
"We'd like to ask people in the affected areas to help each other and act calmly," Suga said in a televised remark.
More than 20 aftershocks hit Nagano following the first big strike Saturday.
The meteorological agency warned strong aftershocks could still occur in the coming week.
"It is fully possible that houses already damaged by the main quake could be dealt further blow by aftershocks," the official at the press conference 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.
Other nuclear plants were also intact.
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 that sparked the Fukushima atomic disaster and left 18,000 people dead or missing.
source: www.abs-cbnnews.com
