The Japan Meteorological Agency on Saturday issued the highest alert level for heavy rain across several cities in the Ishikawa prefecture, including hard-hit cities Suzu and Wajima on the northern coast of the Noto peninsula.
The agency has since downgraded the heavy rain alert, and kept landslide and flooding warnings in place.
Numerous roads are blocked after being flooded with mud and debris (AP PHOTO)
In Suzu, one person died and another was missing after being swept in floodwaters. Another went missing in the nearby town of Noto, according to the prefecture.
In Wajima, rescue workers were searching for four people missing following a landslide at a construction site. They were among 60 construction workers repairing a tunnel damaged by January's quake.
Another person is missing due to floods at a different location in the city.
NHK footage at a coastal area of Wajima showed a wooden house torn and tilted after it was apparently hit by a landslide. No injuries were reported from the site.
In Noto town, two people were seriously injured by a landslide while visiting their quake-damaged home.
At least 16 rivers in Ishikawa breached their banks on Saturday, according to the Land and Infrastructure Ministry. Residents were urged to use maximum caution against possible mudslides and building damage.
At least 16 rivers in Ishikawa have breached their banks. (AP PHOTO)
By late afternoon Saturday, about 1350 people were sheltering at designated community centres, school gymnasiums and other town facilities.
About 50cm of rain has fallen in the region over the last three days.
"Heavy rain is hitting the region that had been badly damaged by the Noto earthquake, and I believe many people are feeling very uneasy," Chief Cabinet Secretary Yoshimasa Hayashi said.
A number of roads flooded by muddy water were also blocked and Hokuriku Electric Power Company said more than 5000 homes were still without power on Sunday. Traffic lights were out in the affected areas. Many homes were also without a water supply.
Heavy rain also fell in nearby northern prefectures of Niigata and Yamagata, threatening flooding and other damage and suspending train operations, including the Yamagata Shinkansen bullet trains, officials said.
A 7.6 magnitude earthquake struck the region on January 1, killing more than 370 people and damaging roads and other key infrastructure.
