The 6.5 magnitude quake hit the central Ishikawa region mid-afternoon on Friday at a depth of 12km, according to the Japan Meteorological Agency.
More than 50 aftershocks, some of them strong, had occurred by this morning, the agency said, as it warned that heavy rain could trigger landslides in the area.
At least 29 people had been injured, Japan’s disaster management agency said today.
“Our staff are out checking damage from the quake,” an official from Suzu in Ishikawa prefecture, the hardest-hit city, told AFP.
Two people trapped inside destroyed buildings were rescued, he said, and around 50 people had moved to evacuation centres set up at schools and the city hall.
TV footage showed a grocery shop strewn with broken wine bottles and other products that had fallen from shelves.
Some residents were seen clearing rubble in the rain after their wooden houses were partially destroyed.
“I asked a carpenter for a makeshift fix of the house, and the house is now covered with a blue tarp to protect it from rainwater,” one man told public broadcaster NHK.
Water outages affected more than three dozen households in Suzu, officials said today.
They added that the city had provided temporary public supplies after running water had turned brown in parts of the region.
The quake registered an upper six on the Japanese Shindo seismic scale, which goes up to a maximum of seven.
Earthquakes are common in Japan, which sits on the Pacific “Ring of Fire”, an arc of intense seismic activity that stretches through South-east Asia and across the Pacific basin.
The country has strict construction regulations intended to ensure buildings can withstand strong quakes and routinely holds emergency drills to prepare for a major jolt.
A 6.9 magnitude quake struck a fishing village in the same region in 2007, injuring hundreds and damaging more than 200 buildings on the Noto peninsula – a scenic area in central Japan.
“I express my heartfelt condolences to the person who died and offer my sympathies to those who were hit by the disaster,” Prime Minister Fumio Kishida said on Friday.
“The government will continue taking measures with a sense of urgency while closely communicating with (officials) at the scene,” Kishida told reporters.
Japan is haunted by the memory of a massive 9.0 magnitude undersea quake off its north-east in March 2011, which triggered a tsunami that left around 18,500 people dead or missing.