The heaviest rain in decades pounded the country, threatening to worsen conditions in the wake of Typhoon Etau, which smashed through Japan earlier this week bringing strong winds and travel chaos.
At least 22 people, including a pair of eight-year-old children, were missing in disaster-struck Joso city, public broadcaster NHK said, quoting officials in the area which lies about 60 kilometres (37 miles) outside Tokyo. Another person was missing in a northern prefecture.
Joso, a community of 65,000 residents, was hammered Thursday when a levee on the Kinugawa river gave way, flooding an area that reportedly spans 32 square kilometres (12 square miles) and includes 6,500 homes.
Dramatic aerial footage showed whole houses being swept away by raging torrents in scenes eerily reminiscent of the devastating tsunami that crushed Japan's northeast coast four years ago.
Desperate Joso residents waved towels as they stood on balconies trying to summon help, while military dinghies ferried dozens of people to safety, and helicopters plucked individuals from rooftops.
Others took to social media on their smartphones to beg for help.
Survivors of the flooding recounted horrific scenes as the muddy brown waves swirled around their doomed houses, while trees were uprooted and cars bobbed in the dirty water.
An evacuated Joso resident said she was anxiously awaiting details about her family at an emergency shelter, after leaving her husband and children to go shopping Thursday morning. She was unable to return home due to the flooding.
"I have been here since yesterday morning... And I do not have any news about my family," said the woman in her sixties who gave her last name as Furuya.
Top government spokesman Yoshihide Suga said some 5,800 troops, police and firefighters were dispatched early Friday to flooded areas where rescuers had worked through the night.
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