Weather officials are calling for caution as continuing heavy rain may cause landslides, flooding in low-lying areas, and swollen rivers till midweek.
The Meteorological Agency says the lingering seasonal rain front is bringing active rain clouds to parts of eastern and western Japan.
Warm, damp air is blowing into the front, creating an unstable atmospheric condition.
It has brought torrential rain to the southern main island of Kyushu.
Between 5 a.m. and 6 a.m. Sunday, 67 millimeters of rain was recorded in the city of Uki in Kumamoto Prefecture.
Intermittent heavy rain is expected to fall till midweek in parts of western and eastern Japan. Intense rain of 70 millimeters per hour could fall in northern Kyushu.
In the 24 hours up to Monday morning, as much as 300 millimeters of rain is expected in northern Kyushu and 200 millimeters in Shikoku and southern Kyushu.