Prime Minister Shinzo Abe canceled an overseas trip because of the disaster, a ruling party source said. Road blockages and power outages have also forced many companies to halt operations until the circumstances lift.
Scores of patients‚ some still in their pajamas‚ and nurses were rescued from the isolated Mabi Memorial Hospital in boats rowed by members of Japan's Self Defence Forces.
More than 50 people were unaccounted for as of Tuesday evening, many in the hardest-hit Hiroshima area.
The death toll has already exceeded the recent most deadliest rain-related disaster in 2014, when at least 74 people were killed in landslides caused by torrential downpours in the Hiroshima region.
But they were soon marooned by rising flood waters and a military boat had to pluck them from the second floor of their house, where they had taken refuge.
Debris fills a small village following heavy rains Sunday, July 8, 2018, in Kuchita-Minami, Asakita-ku, Hiroshima, Japan.
People prepared for risky search and cleanup efforts in southwestern Japan on Monday, where several days of heavy rainfall had set off flooding and landslides in a widespread area.
Rescue workers said it was still possible that survivors could be found, but acknowledged the odds were getting longer.
The heavy rains triggered massive landslides in some areas: "There have been massive flooding and landslides", government spokesman Yoshihide Suga told a news conference.
"So many people called". 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.
Koji Tsunomori, 54, lost his 44-year-old wife Nana, whom he married around three weeks ago, in a mudslide in the town of Kumano in Hiroshima.
Residents try to upright a vehicle stuck in a flood hit area in Kurashiki, Okayama prefecture. The floods are considered the worst the country has seen in 35 years.
It's the worst weather-related disaster in the country since 2011, when almost 100 people were killed by two typhoons in August and September.
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.
President Cyril Ramaphosa sent his condolences to Japan on Sunday after at least 69 people were killed and 1‚850 were stranded in the western Japanese city of Kurashiki.
While persistent rain had ended, officials warned of sudden showers and thunderstorms as well as more landslides on steep mountainsides saturated over the weekend.
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.