More than 540 millimetres of rainfall in the past 72 hours to Sunday morning was recorded in Wajima.
The same region was hit by an earthquake earlier this year that killed at least 318 people.
For climate change news and analysis, go to News24 Climate Future.
Floods and landslides left one dead and at least six missing in central Japan, with rescue and recovery teams at work on Sunday in a remote peninsula already devastated by a major earthquake earlier this year.
"Unprecedented" heavy rains that lashed the area from Saturday began to subside, leaving muddy scenes of destruction as the national weather agency urged residents to stay vigilant for loose ground and other dangers.
Subscribe our newsletter to stay updated
Thank you for subscribing!
Subscribe our newsletter to stay updated
Thank you for subscribing!