Unprecedented torrential rain has caused rivers to burst their banks, sweeping away roads and houses, and destroying schools.
Thousands of soldiers and others were scrambling today to reach people cut off by torrents of swirling water or threatened by landslides, and had rescued 250 people, the government said.
"We are in an extremely serious situation," Deputy Prime Minister Taro Aso said, warning of the danger of collapsing hillsides and adding "many people are still missing".
Downpours will likely continue through Friday, the agency said as the region grapples with the aftermath of a typhoon that raked the country this week.
Authorities lifted "special" heavy rain warnings for the hardest hit prefectures of Fukuoka and Oita, although other warnings, such as for rain, landslides and flooding, remained in place.
One man was found dead in the city of Asakura in Fukuoka prefecture, while another died in a landslide in Hita in Oita prefecture, officials said.
Those included a child reportedly carried off by a fast- flowing river and a couple who had not been seen since their house was swept away.
Television footage showed rolling waves from swollen rivers hitting residential areas, tearing up roads and inundating farmland.
Asakura was among the hardest hit with footage showing floodwaters surging through the streets.
Ryoichi Nishioka, who grows flowers in the city, said he tried to save them from damage amid fast rising waters the night before.
Nishioka, 67, also described helping a man who clung to an electric pole as muddy waters rampaged through the area on Wednesday night.
"We had a blackout, so I used a flashlight from the second floor and shined light for him," he said. "I was calling out to encourage him for three hours from 9pm to midnight.
"I shouted: 'Hang in there!'" The man was ultimately rescued, Nishioka said.
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