Rainy conditions were forecast to continue into July 4.
Since last Friday, some areas of Kyushu have received as much as 1,000 mm of rain, or more than double the usual volume for all of July, public broadcaster NHK said.
The warnings have come after days of heavy rain has increased the chances of flooding in the area.
The Japanese island of Kyushu, inhabited by 13.3 million residents, was lashed by more than 300 millimeters (11.8 inches) of rain in multiple locations Thursday.
The entire populations of Kagoshima city, Kirishima and Aira were ordered to evacuate, with another 930,000 people in the south of the island also being advised to flee. "For those living in risky areas, such as near a cliff or river, please evacuate at once".
Television footage showed rivers filled with fast-moving brown water, but none had overflowed their banks as of Wednesday evening, although one low dike had broken.
One woman has so far been killed in the rains that began at the weekend, after her house was buried in a landslide.
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Officers grabbed the cart after it became wedged in the broken glass and repelled the protesters with pepper spray. Meanwhile, crowds gather in Victoria Park for the annual July 1 march. "She is protected by our flawed system".
Several small landslides were reported, including one that swept away two cars.
Some 14,000 troops have been placed at the ready for necessary rescue work.
"Evacuate early without waiting for it", he urged.
Deputy Chief Cabinet Secretary Yasutoshi Nishimura told reporters Thursday that four people were injured in the hardest-hit southern prefecture of Kagoshima, but none seriously.
"Please take action to protect your lives", Prime Minister Shinzo Abe said on Wednesday, according to Japan Times.
Japanese Prime Minister Shinzo Abe addresses during the XXIII ANOC General Assembly in Tokyo, Japan, on November 28, 2018.
In the past, the baiu season has caused devastating natural disasters.