"Please take care of yourself and those who you care about to protect your and their lives", Mori said at the emergency news conference, while issuing an evacuation order to Kagoshima's 590,000 residents.
All 590,000 residents of the city of Kagoshima were told to evacuate and were seen filling evacuation shelters.
The country's Fire and Disaster Management Agency issued a directive for more than 1 million residents to evacuate to designated shelters in three southern prefectures.
More than 1 million people in southern Japan were ordered to evacuate Wednesday as the region was hit with almost a month's worth of rain in a single day, according to local officials.
A woman in her 80s died after her home was buried in a landslide in the city of Soo, The Japan Times reported.
According to the Japan Times, Kagoshima Governor Satoshi Mitazono mobilized the Self-Defense forces to assist with disaster relief.More news: The Rise Of Skywalker Will Reveal Who Rey's Parents Are
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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.
Reportedly a month's worth of rain could hit parts of Kyushu in just 24 hours.
Kagoshima, Kumamoto and Miyazaki prefectures faced the prospect of being lashed by more than 80 millimeters of heavy rain per hour through July 4, the JMA said.
It said a rainy front is expected to stay over the Japanese archipelago through Saturday, and could also drench eastern Japan.
Rescue workers and local residents watch the Wada River, which has been swollen due to heavy rain in Kagoshima.
It was the highest death toll caused by rainfall in Japan since 1982.