Emergency warnings of severe rain in 11 prefectures - the most since a new warning system was introduced in 2013 - had been lifted by evening, but advisories of heavy rain and landslides remained in effect in many areas. The rains began Thursday and continued into Sunday in many areas.
Television footage showed muddy water flowing out of rivers in parts of the region, including the scenic Arashiyama area in western Kyoto where riverbanks and streets were flooded.
Thirteen were confirmed dead in Hiroshima Prefecture.
The Japan Meteorological Agency said three hours of rainfall in one area in Kochi prefecture reached an accumulated 26.3 centimeters (10.4 inches), the highest since such records started in 1976.
"The situation is extremely unsafe", wrote a Twitter user in Kochi, a city on the smallest main island of Shikoku, where the rain has been especially intense.
A 52-year-old woman in Kyoto was found dead by a river on Friday, while in neighbouring Hyogo prefecture a construction worker was swept away by flood waters and died.
"It's very painful", said one elderly man watching nearby."I have a granddaughter the same age". "I have a granddaughter the same age". The younger, a first-grader, was a star and the hope of the depopulated island, the principal told NHK.
Chief Cabinet Secretary Yoshihide Suga said around 48,000 police, fire fighters and members of the Self-Defence Forces were responding to more than 100 landslides and other appeals for help.
"The situation is extremely serious", Shinzo Abe, the prime minister, said as he called for an "all-out" rescue effort.
As much as 300 mm rain is predicted by Monday morning in parts of Shikoku island.
Another three million have been advised to flee. NHK said a woman died in her home in Hiroshima when it got buried in a mudslide.
Four people in Ehime, Hiroshima and Yamaguchi prefectures were in critical condition after being injured in landslides, it added.
Carmakers including Mazda and Daihatsu suspended operations at several plants last Saturday.
People wait to be rescued on the roof of a house nearly submerged in floodwaters caused by heavy rains in Kurashiki, Okayama prefecture, southwestern Japan on Saturday.
REUTERS/Issei Kato REFILE CORRECTING TYPO Japan Self-Defense Force soldiers carry a boat for their rescue work at a flooded area in Mabi town in Kurashiki, Okayama Prefecture, Japan, July 8, 2018.
Japanese military personnel evacuate residents in Kurashiki, Okayama prefecture.
"Around 1,000 people were seeking rescue by Sunday morning, but we don't yet have a complete picture of the disaster, which is enormous", Mutsunari Imawaka, a spokesman for the prefecture's disaster management office, told AFP.