The strongest evacuation warning, Level 5, was issued on Saturday to more than a million people across the prefectures of Saga, Nagasaki, Fukuoka, and Hiroshima, according to public broadcaster NHK.
The next-strongest warning, Level 4, was issued to 17 other prefectures, affecting more than 4 million residents.
The country’s meteorological authority, which issued the warnings, said in a statement that the rain front could stay over the country for about a week, according to Reuters.
Photographs from hard-hit provinces show residents wading through thigh-high water in flooded streets, carrying children and belongings. Firefighters and other emergency workers were also rescuing stranded residents, loading them onto inflatable boats.
Water levels are still rising in several rivers, threatening to overflow onto the surrounding roads.
Some cities on the southern island of Kuyshu recorded more than 40 millimeters (about 1.6 inches) of water in one hour on Saturday. Up to 250 millimeters (9.8 inches) could fall on the island in the 24 hours through Sunday morning, national weather officials say.
Adachi Yushi, the head of weather monitoring at the Meteorological Agency, called the rain “unprecedented” and asked people to follow evacuation orders, according to NHK.
Prime Minister Yoshihide Suga tweeted on Friday that he had set up a disaster control center to coordinate with local and prefecture authorities.