The quake struck at 10:08 pm local time Saturday at a depth of 10 kilometres (six miles) at the epicentre, in the north of Nagano Prefecture, northwest of Tokyo, according to the US Geological Survey.
The government confirmed Sunday that the quake injured 39 people, destroying houses and snapping water pipes, with the worst damage in mountainous areas.
In Nagano Prefecture’s famous Hakuba Village — a popular ski resort that hosted part of the 1998 Winter Olympic Games — many homes were toppled and destroyed, local authorities said. Bird’s-eye footage by public broadcaster NHK showed houses reduced to rubble.
Around 30 people were trapped in the collapsed village houses soon after the quake, but were all rescued, Jiji Press said.
The meteorological agency warned strong aftershocks could still occur in the coming week.
There was no damage to 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 plant disaster and left 18,000 people dead or missing. (AFP)