Hiroshima and Ehime prefectures were some of the hardest hit, though nine others were also heavily impacted.
The severe rain caused rivers to overflow, in some cases covering whole towns. Three people died at the scene in Ayabe City in Kyoto Prefecture, where two houses collapsed.
Almost 2 million people have been asked to evacuate the affected areas.
Even as the rains let up, authorities warned the downpours had loosened earth on hillsides and mountain slopes creating new risks.
The number of households that still had no running water came to 206,868 in Hiroshima Prefecture, 21,610 in Ehime Prefecture and 9,609 in Okayama Prefecture, according to the Health, Labor and Welfare Ministry. Kyodo reported that 13 railroad operators were suspending services on 37 routes in western Japan and elsewhere on Monday.
To safeguard their workers, some major businesses in the disaster-hit regions have halted production, including at Mitsubishi Motors Corp. and a subsidiary of Toyota Motor Corp.
Images from Kuyashiki, a city on the southern coast of Okayama Prefecture, show cars overturned or buried in mud.
He says the United Nations chief "commended the government's efforts to help people affected and expressed his admiration for the domestic search and rescue teams helping those in need".
Local government officials said pumping trucks were being deployed to help restore access to some of the worst-hit areas in the area, and with the rains stopped, water was starting to recede.
In the city of Kurashiki, the flooding engulfed entire districts at one point, forcing some people to their rooftops to wait for rescue. A series of quakes in Kumamoto in 2016 led to the deaths of more than 200 people, according to the Japanese Red Cross Society.
Millions of people were advised to evacuate their homes.
Hiroshima resident Akira Tanimoto on Monday returned to the apartment complex where he and his wife live to check on their unit and their pet birds, which they initially had to leave behind, the Associated Press reported.
During a meeting of the government's crisis response unit in Tokyo on Tuesday, Prime Minister Shinzo Abe pledged to swiftly provide emergency relief by using reserve funds without waiting for requests from local governments.
"I'm afraid elderly people who were living alone may have failed to escape", said Yamanaka, 53. "Some people have been isolated, calling for rescue".
Three days since the disaster struck, Japan's Self-Defense Force, firefighters, and rescue dogs are working against time searching through debris for survivors.
In areas ravaged by the rain disaster, infrastructure such as roads, railways, waterworks and power supplies have been disrupted.
Japan's government set up an emergency management center at the prime minister's office and some 54,000 rescuers from the military, police and fire departments were dispatched across a wide swath of southwestern and western Japan.
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