Although evacuation orders were scaled back from the weekend, almost 2 million people still face orders or advice to keep away from homes, fire and disaster officials said.
Most of the deaths were reported in Hiroshima and Ehime Prefectures, though eight prefectures were impacted.
Japan monitors weather conditions and issues warnings early, but its dense population means every bit of usable land is built on in the mostly mountainous country, leaving it prone to disasters.
Several major manufacturers, including carmakers Daihatsu and Mitsubishi, suspended operations at plants in the affected areas.
Aerial photos of an area of Hiroshima hit by flash flooding and landslides show homes that have been tossed upside down, and others that have been reduced to shattered piles of lumber and roof tiles.
Some residents in Hiroshima prefecture said they were caught off guard in a region not used to torrents of rainfall, which began Friday and worsened through the weekend. (Reuters/Issei Kato) A truck stranded by floods on July 9.
Minoru Katayama, 86, rushed back to his home in Mabi city, in Okayama prefecture, and found his 88-year-old wife, Chiyoko, collapsed on the first floor.
Policemen check a damaged auto following heavy rains and flooding in Hiroshima.
The town of Kaita, on the outskirts of Hiroshima, was also heavily damaged by flooding and landslides.
In large parts of Hiroshima, water streamed through a residential area, strewn with fallen telephone poles, uprooted trees and mud.
The compound of a junior high school is flooded after heavy rains in Kurashiki, Okayama Prefecture, southwestern Japan.
A resident walks across scattered debris in a flood hit area in Kurashiki, Okayama prefecture.
In seven prefectures, about 5,100 homes faced blackout as of Monday evening, according to the Ministry of Economy, Trade and Industry.
"My body is sticky because I haven't taken a bath and I left my glasses behind and can't see anything", said a woman in her 70s, who was rescued by Self-Defense Forces personnel after being found trapped in her home in water up to her chest.
The downpours have also hit businesses, though some companies have already resumed suspended operations.
The disaster in western Japan has claimed the lives of 120 people with 80 missing and tens of thousands displaced.
At least 100 people have been killed in days of record rains that have devastated parts of Japan, and at least 21 people are missing, local authorities confirmed on Monday.
The brewery is flooded, which damaged raw rice stored in its warehouse, and power has not been wholly restored, president Kazuhiro Sakurai told NHK.