TV footage shows brown, rapidly flowing, flooded rivers threatening buildings in Kagoshima.
The heavy rainfall comes after large parts of Japan experienced a brutal heatwave where a record temperature of 41.8 degrees was set last week.
Kagoshima "is experiencing heavy rain that has never been seen before", says an official from the Japanese Meteorological Agency (JMA) at a press conference.
The local fire and disaster agency is now urging 530,000 people in the Kagoshima region and neighboring Miyazaki to evacuate and take alternative measures.
