But that does not mean the danger is over. People are advised to stay away from swollen rivers and evacuate if necessary based on information from local governments.
Officials at the Meteorological Agency point out that people have previously been injured in landslides that occurred several hours after rain stopped.
They say rivers have also previously flooded and caused major damage after emergency warnings were lifted.
The rain in Kyushu is weakening, but water levels in some rivers remain high.
Rain that has fallen in mountainous areas will take time to flow into large rivers, meaning levels may rise at unexpected times.
Maximum rainfall alert issued in parts of Kyushu
People in southwestern Japan are bracing for more life-threatening rain after already being pounded in recent days. Authorities have issued the highest level of alert for some parts of Fukuoka and Oita Prefectures on the island of Kyushu.
Some rivers have flooded in Fukuoka, Saga and Oita prefectures in Kyushu. Others are close to flooding, including in Yamaguchi Prefecture on the main island of Honshu.
Authorities have issued landslide warnings in parts of those prefectures, and also Hiroshima Prefecture in Honshu. They are urging residents to move to upper floors and stay in rooms away from slopes.
Dangerous conditions through Tuesday
Extremely heavy rain is expected in northern Kyushu through Monday evening. The weather front is expected to remain stationary until Tuesday.
Rainfall of 70 millimeters per hour is expected through Monday evening in some parts of northern Kyushu and Yamaguchi Prefecture.
And in the 24-hour period through Tuesday noon, rainfall is expected to reach up to 180 millimeters in northern Kyushu, 120 millimeters in Yamaguchi and 80 millimeters in the Chugoku region.
Floods as of 3 p.m.
The highest flood alert level, which means disasters have already occurred, has been issued for the Yamakuni and Kagetsugawa rivers in Oita Prefecture; the Tokusuegawa and Jobarugawa rivers in Saga Prefecture; and the Koishiwara and Kose rivers in Fukuoka Prefecture.