The prefectures of Okayama, Hiroshima and Yamaguchi were the hardest hit, with pictures showing extensive damage especially in Okayama.
The heavy rainfall stemmed from the remnants of a typhoon that hit south-western Japan last week.
Tens of thousands of rescue and recovery workers were digging through the debris as the search entered its fifth day, The Associated Press reports.
Media captionAbout two million people were evacuated after rivers burst their banks.
Authorities warned landslides could strike even after the rain subsides as the calamity shaped up to potentially be the worst in decades.
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.
Emergency service workers pass a damaged road following a landslide, on July 10, 2018 in Yanohigashi near Hiroshima, Japan.
Automakers including Mazda Motor Corp (7261.T) and Daihatsu Motor Co suspended operations at several plants on Saturday due to a shortage of parts or unsafe conditions.
In Okayama prefecture, rescue workers flew in helicopters over areas that are still under flood water and otherwise unreachable, looking for signs of life. Six people are in critical condition, and dozens are still missing, the public broadcaster NHK reported on Sunday.More news: May says Brexit plan delivers 'people's vote'
People fled to rooftops and balconies in the city of Kurashiki, at the mouth of the Takahashi River, about 670 kilometers (415 miles) from Tokyo.
More than 70,000 rescue workers, including the fire service and the army, are now involved in relief efforts. More than 1,000 people were left temporarily on building roofs while waiting to be rescued. Nationwide, some four million people have been advised, though not ordered, to evacuate their homes and about 30,000 are in temporary evacuation centers, news agencies reported.
Some were already feeling unwell under the summer heat as they lined up in the open air for a water supply truck at an evacuation center in Mihara, Hiroshima Prefecture, despite the presence of a portable air conditioning device.
Prime Minister Shinzo Abe plans to visit the devasted areas.
"People believe Okayama is very safe, nobody thought that [a disaster] would happen to this city", Yusuke Fujii, who lives in Osaka but travelled to Okayama to visit his grandmother, told the BBC. "Some people have been isolated, calling for rescue".
The landslides and flooding across much of western Japan have killed at least 134 people, Chief Cabinet Secretary Yoshihide Suga told a news conference.
In areas ravaged by the rain disaster, infrastructure such as roads, railways, waterworks and power supplies have been disrupted.
"The rescue and lifesaving operation is now a race against the clock", Prime Minister Shinzo Abe said.