By Saturday morning, more than 1.6 million people had been ordered to evacuate their homes for fear of flooding and further landslides, with 3.1 million more advised to leave, the Fire and Disaster Management Agency said.
Japan's Meteorological Agency retained special weather warnings for three prefectures on the main island of Honshu, down from five, and urged vigilance against landslides, rising rivers and strong winds amid what it called "historic" rains. Authorities warned landslides could strike even after rain subsides as the calamity shaped up to be potentially the worst in decades.
At least 38 people have died, four people are said to be in a serious condition and another 47 remain missing, the public broadcaster NHK reported. In all, eight prefectures have been affected, including Kyoto and Hiroshima.
These prefectures include those in the Kansai region, including Osaka, which is still reeling from a powerful quake that hit the area in June. Abe asked members of his Cabinet to do everything they can to assist the search and rescue work.
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.
Residents are evacuated to a safer place from floodwaters caused by heavy rains in Kurashiki, Okayama prefecture, southwestern Japan.
The Kyodo news agency said around 1,850 people in the area had been trapped on the roofs of buildings, and that the land ministry planned to mobilise 20 trucks to begin pumping water out of flooded areas and restore access.
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In Ehime Prefecture, a woman was found dead on the second floor of a home buried by a landslide.
Residents look at a flooded road and houses in Kurashiki, Okayama, prefecture on July 7, 2018.
"This is heavy rain at a level we've never experienced", a JMA official said as the agency issued warnings in Okayama, Hiroshima, Tottori, Fukuoka, Saga, Nagasaki, Hyogo and Kyoto prefectures.
Japan's government set up an emergency management centre at the prime minister's office and some 54,000 rescuers from the military, police and fire departments were dispatched across a wide swath of southwestern and western Japan. Some 30,000 people remained in shelters on Sunday, while the evacuation orders and advisories were issued for almost 6 million people, according to the Fire and Disaster Management Agency.
Kochi Prefecture, on Shikoku, issued landslide warnings nearly over the entire island. 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.
It is the deadliest rain event in Japan since 2014, when at least 74 people died due to landslides that were triggered by torrential downpours in the Hiroshima region.