Two people were confirmed dead on Wednesday as heavy rains pounded southwest Japan, prompting flood and landslide warnings and orders for 670,000 people to seek safety.
Nearly a million more people were advised to leave their homes after the country's weather agency raised the alert to its highest level for parts of northern Kyushu.
The emergency warning is issued "if there is a significant likelihood of catastrophes".
Officials confirmed two deaths, one in western Saga prefecture where a man was found in a car that had been swept away.
A second man died in Fukuoka as he tried to escape from a car trapped in rising floodwaters.
Government spokesman Yoshihide Suga said a third person, in Saga, was in a state of "cardiorespiratory arrest" -- a term usually employed by Japanese officials to indicate a person's death before it is officially confirmed by a doctor.
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"There are many reports of damage in different areas due to flooding of rivers, landslides, and submerged houses, and there is a possibility of serious damage occurring in the coming hours," Suga added.
Evacuation orders and advisories issued by local authorities are not mandatory, although officials urge residents to heed them.
For those leaving after such warnings, government shelters are available, and some choose to stay with friends and family as well.
The fire and disaster management agency said it had already received multiple reports of flooded houses in Saga and Nagasaki prefectures.
"We are seeing unprecedented levels of heavy rains in cities where we issued special warnings," a spokesman for the Japan Meteorological Agency told reporters.
"It is a situation where you should do your best to protect your lives," weather agency official Yasushi Kajiwara said.
He also urged those living in areas currently under evacuation advisories to act quickly.
In Saga, a mother wearing a life vest in a rescue boat told public broadcaster NHK she had been saved from the floodwaters.
"I was so scared as I have a little child. I'm worried there could be worse damage because there's an ongoing power outage," she said.
Elsewhere, a man in a shelter in Saga said he was sleeping as the floodwater entered his home.
"When I woke up, water surged to my feet," he told NHK.
"I've never seen anything like this. It's important to evacuate early."