One woman, believed to have been in her 70s, was rescued after a mudslide hit her home in Kagoshima but was later confirmed to have died.
Rescuers work on the rooftop of the house damaged by a landslide in Soo, Kagoshima prefecture, western Japan, Thursday, July 4, 2019.
People living in Kagoshima and Miyazaki on the southern island of Kyushu have been told to move to safety immediately.
About 900mm (35 inches) of rain has fallen on the southernmost main island of Kyushu since late June, according to state broadcaster NHK.
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.
Sections of the Shinkansen bullet train on the southern island of Kyushu were disrupted by the heavy rain, which forced more than 150 schools to cancel classes, Kyodo news agency reported.
Videos filmed by residents were circulated on social media showing a river in Kagoshima swollen with muddy, brown water threatening to overrun its banks.
Japan's Meteorological Agency said a number of places within the prefecture, which has a population of 1.6 million people, were at risk of landslides and flooding.
All 590,000 residents of the city of Kagoshima were told to evacuate and were seen filling evacuation shelters.
Deputy Chief Cabinet Secretary Kotaro Nogami said 14,000 ground troops were standing by for emergency rescue and search operations if needed.
He also urged residents to use caution and try to evacuate early "to protect your lives" rather than waiting until the last minute.
Landslide warnings remained in effect for Kagoshima, Miyazaki, and Kumamoto prefectures.
"Please take action to protect your lives", Prime Minister Shinzo Abe said on Wednesday, according to Japan Times.
In the past, the baiu season has caused devastating natural disasters.