NHK and other news agencies reported on September 23 that six people were confirmed dead and 10 missing in the heavy rains. Kyodo news agency reported that more than 100 communities were cut off by road closures after nearly two dozen rivers burst their banks.
Two of the victims died near a landslide-hit tunnel in Wajima city, Ishikawa prefecture, which is still undergoing repairs after the New Year's earthquake.
Rainfall in Wajima and the nearby city of Suzu reached double the average for September. The Japan Meteorological Agency downgraded the "special warning" for the area to "warning", but advised residents to remain vigilant.
Prime Minister Fumio Kishida has instructed officials to monitor damage and cooperate with local authorities as rains caused by a tropical depression hit, as the region is still recovering from an earthquake in January.
Heavy rain has been falling in Ishikawa since September 21, with more than 540mm recorded in Wajima City in 72 hours. This is the heaviest continuous rainfall since comparable data began.
The area is still struggling to recover from a 7.5-magnitude earthquake earlier this year, which toppled buildings, triggered tsunamis and sparked a major fire.
Floodwaters submerged emergency housing built for people who lost their homes in the earthquake earlier this year that killed at least 374 people, according to Ishikawa prefecture.
According to Hokuriku Electric Power Company, on September 23, up to 4,000 households lost power after the rain.
Akemi Yamashita, a 54-year-old Wajima resident, said she was driving on September 21 when "within 30 minutes, water flooded the street and quickly rose to half the height of the car."
"I talked to other residents of Wajima yesterday and they said, 'It's heartbreaking to live in this city'. I was moved to tears when I heard that," she said, describing the earthquake and flooding as "like a scene from a movie".
In Wajima on September 22, broken branches and a large uprooted tree piled up on a bridge over a river where brown water flowed fiercely.
The military was sent to Ishikawa to join rescue efforts over the weekend, as tens of thousands of residents were urged to evacuate.
Scientists say human-caused climate change is increasing the risk of heavy rains because the warmer atmosphere holds more water.
Areas under emergency warning zones have seen "heavy rain at an unprecedented level", said Japan Meteorological Agency (JMA) weather forecaster Satoshi Sugimoto, adding: "This is a situation where you have to secure safety immediately".