The heaviest rain in half a century fell on parts of Kyushu on Thursday, the Meteorological Agency said.
Mount Nagaura in the city of Nagasaki saw 205 mm of rainfall and Sakai city in Nagasaki Prefecture recorded 155.5 mm over the course of three hours, both topping record levels dating back 50 years.
The agency issued a heavy-rain warning for the three northern Kyushu prefectures of Fukuoka, Saga and Nagasaki.
In the prefectural capital of Nagasaki, some houses were inundated below and above floor level. Roads flooded and there were landslides in parts of the city.
The agency warned of another downpour on Friday in western Japan, urging residents to pay attention to possible river flooding, landslides, lightning strikes and tornadoes.