Television footage from various communities in Kumamoto prefecture showed houses, stores and vehicles submerged in about a metre (3.3 feet) of water.
Surging rivers swept away vehicles and damaged roads.
More than 40 centimetres (15.9 inches) of rain fell over 12 hours in Kumamoto prefecture's hardest-hit Tamana city, a record for the area according to the Japan Meteorological Agency.
By Monday morning, evacuation advisories and warnings were issued to more than three million residents in the southwestern regions, the Fire and Disaster Management Agency said.
While the most severe warnings were lifted in all areas, lower-level alerts including some evacuation advisories remained in the evening.
Although heavy rain in Kumamoto has slowed, active rain fronts could cover other parts of Japan at any time, Shuichi Tachihara, chief of forecasting at JMA, told a televised press conference.
"Heavy rainfall to date has loosened the ground in some areas and caused water levels to rise in some rivers," he said.
"The risk of disasters may increase again in the future, even with less rainfall. Please continue to be extremely vigilant for landslides, and be aware of rising river levels and flooding."
Local media said Monday afternoon that emergency workers found one person unresponsive in Kosa town in Kumamoto, near a place where a man had gone missing earlier in the day.
He disappeared in a landslide which hit when he was standing outside his home, while his wife and two children were safely inside their car, Kumamoto's RKK television station said.
The town's officials could not immediately confirm the report.
In Misato town, also in Kumamoto, an elderly man was rescued after being trapped inside his house when it was struck by a landslide.
"The rain was so heavy that I couldn't see what was in front of me for four to five hours," Misato town official Kazuhiro Masunaga told AFP.
Two people in Fukuoka city were swept away in a surging river Sunday and remained missing, national broadcaster NHK reported.
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