Heavy rain Saturday night to early Sunday in northern Fukui Prefecture left at least three people dead, and some 55,000 households were advised to evacuate.
Officials in the town of Imadate said a 66-year-old man was crushed to death under a concrete wall that collapsed because of heavy rain. Meanwhile, the body of a 65-year-old man was found in the Asuwa River in the town of Miyama, police said.
In the town of Shimizu, a 76-year-old man was killed after falling into an irrigation ditch.
According to the Japan Meteorological Agency, the risk of mudslides has risen to the worst level in years in mountainous areas in the prefecture.
Meanwhile, in Niigata Prefecture, the death toll from torrential rains since early last week reached 15 on Sunday as one more body was found, police said.
As of 6 p.m. Sunday, evacuation orders remained in effect for some 11,000 households in six municipalities in Niigata Prefecture.