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Dramatic footage shows people wading through floods in the coastal region of Ishikawa, where communities were reeling from an earthquake on New Year's Day which saw hundreds killed.
Aerial shots show cars and homes, including temporary accommodation used by people who were stranded during the earthquake, submerged by floods.
The highest level of alert for heavy rain has been issued for several cities in the region, including Suzu and Wajima on the northern coast of the Noto peninsula.
In Suzu, one person has died and another has been missing after being swept into floodwaters.
Another has been missing in the nearby town of Noto, according to the prefecture.
Four people went missing following a landslide at a construction site in Wajima, while another person has been reported missing from a separate location in the city.
About 6,500 homes have been left without power due to the storm, according to the Hokuriku Electric Power Company. Many homes were also without water supply.
Communities in Ishikawa have been trying to bounce back from the effects of the 7.6 magnitude earthquake which struck on 1 January, killing more than 370 people and damaging roads and other key infrastructure.
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At least 12 rivers in Ishikawa breached their banks as of late Saturday morning, according to the Land and Infrastructure Ministry.
Residents have been urged to use maximum caution against possible mudslides and building damage.
By late afternoon Saturday, about 1,350 residents were taking shelter at designated community centres, school gymnasiums and other town facilities, authorities said.
Up to 20 centimetres (7.8 inches) of rainfall are predicted in the region within the next 24 hours through Sunday noon, the Japan Meteorological Agency (JMA) said.
"Heavy rain is hitting the region that had been badly damaged by the Noto earthquake, and I believe many people are feeling very uneasy," said Chief Cabinet Secretary Yoshimasa Hayashi.