Japan's meteorological agency says 110 millimeters of rain fell in one hour in Fukuoka and Saga Prefectures in northern Kyushu.
The agency has issued warnings for flooding and landslides in the area.
Weather officials say warm, moist air flowing into tropical storm Danas, which has moved to the Korean Peninsula, caused the unstable atmospheric conditions.
They say a series of rain clouds cover the area.
During the one-hour period through 5:50 a.m. on Sunday, a radar analysis shows that 110 millimeters of rain fell in the city of Kurume in Fukuoka Prefecture, and the city of Tosu in Saga Prefecture.
In the city of Asakura, 88 millimeters of rain was recorded between 5 a.m. and 6 a.m.
The heavy rain has not let up. In the six-hour period through 9 a.m. the heaviest recorded rain was observed -- 275 millimeters in Kurume and 270 millimeters in Tosu.
Weather officials have issued a landslide alert for some parts of Fukuoka, Saga, Oita and Hiroshima prefectures.
Some rivers in Fukuoka, Saga, Yamaguchi and Hiroshima prefectures have risen above the flood-risk level.
Torrential rain could fall for several more hours in northern Kyushu and more than 50 millimeters of rain per hour, with thunder, could fall in some parts of western Japan through Sunday evening.
During the 24-hour period through Monday morning, the northern Kyushu and Shikoku regions could have as much as 150 millimeters of rain, southern Kyushu could get as much as 120 millimeters and 100 millimeters in the western Honshu region.
Weather officials are warning of landslides and swollen rivers, as well as lightning and gusts of wind.