Eiichi Nakakita, a professor at Kyoto University's Disaster Prevention Research Institute, said 200 mm to 300 mm of rain weakens the ground and makes it more susceptible to landslides.
The evacuation order is issued when a natural disaster is highly likely to occur and municipalities repeatedly urge residents to leave their homes, although the instruction is frequently ignored.
About 793,000 people in Kagoshima remained under evacuation order on Thursday afternoon with more facing lower-level evacuation advisories.
He said rainfall since the weekend has exceeded one metre in areas.
Heavy rain caused flooding and mudslides in southern Japan, injuring four people, damaging dozens of homes and leaving hundreds of others without power.
Several small landslides were reported, including one that swept away two cars and damaged a pre-fabricated shed.
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"The rain was just flowing all over the rice fields", one woman told NHK. "Whoa, the road I take to work is a mess", the user wrote.
Members of the fire department monitor the water level of the Wada River in Kagoshima City, southwest Japan.
Prime Minister Shinzo Abe vowed on Wednesday to spare no effort to protect lives, and has placed 14,000 Self-Defence Force personnel on standby to assist emergency responders.
Bracing for flooding and mudslides, the Japanese authorities directed more than a million people to evacuate the southwestern region of Kyushu island as torrential rains on Thursday continue to jolt the region, triggering heave mudslides and floods.
Japanese Prime Minister Shinzo Abe addresses during the XXIII ANOC General Assembly in Tokyo, Japan, on November 28, 2018.
On Thursday, Toshima in Kagoshima Prefecture received 77 mm of rain per hour and Toba, in the central Japan prefecture of Mie, saw 60.5 mm, while winds of up to 96.12 kilometers per hour were recorded on Miyake Island in the Izu island chain in the Pacific.
The Associated Press and The CNN Wire contributed to this article.