Amid reports of dead and missing, some 1.2 million Japanese were advised to evacuate their homes as monsoon downpours continued to pound the island nation Friday.
Public broadcaster NHK on Saturday said 38 people were dead, four were injured seriously and 47 were missing.
At a meeting with ministers, Prime Minister Shinzo Abe directed them to "prioritise lifesaving and send rescue crews without delay", according to Chief Cabinet Secretary Yoshihide Suga.
In Hiroshima, the body of a man in his 60s was found near a bridge today and officials said another man was killed when a mudslide struck his house.
Some 250 people had to flee their homes and the prefecture identified one fatality as a 52-year old woman.
Since the downpour began Thursday, the weather agency has forecast record amounts of rain through Sunday, warning of flooding, mudslides and lightning strikes. Of those dead by the afternoon, 14 were killed in Hiroshima prefecture, and the rest in Osaka, Shiga, Hyogo, Okayama and Ehime prefectures.
Thousands of police, firefighters and soldiers are taking part in search-and-rescue operations.More news: Tony Parker signs with Charlotte Hornets
In the town of Motoyama, about 600km (370 miles) west of the capital Tokyo, 583mm (23in) of rain fell between Friday morning and Saturday morning, Japan's meteorological agency said.
According to the JMA, an active seasonal rain front is causing torrential rain in most eastern and western regions of Japan, which could continue until Sunday.
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.
"Water came to the middle of the second floor", a woman in Kurashiki, Okayama wrote, posting a picture of her room half swamped by flooding.
Also in Ehime, two elementary-school girls and their mother who got sucked into a mudslide were rescued but their hearts weren't beating, it said.
Defense Minister Itsunori Onodera said another 21,000 troops were on stand-by, adding: "I instructed them to carry out rescue operations by using every possible means of land-sea-and-air forces". Some automakers halted production as the rain and flooding disrupted supply chains and risked workers' safety, Kyodo news agency reported.
As of 11 p.m. on July 6, evacuation orders had been issued to about 2.82 million people and evacuation advisories had been issued to some 4.22 million people in 23 prefectures, a lot of them in the Kinki, Kyushu and Chugoku regions in western Japan.