Mindst 27 mennesker er blevet kvæstede på tværs af 10 amter siden dele af det østlige Japan blev oversvømmet efter en tropisk storm, sagde Brand og Redningstjenesten (Fire and Disaster Management Agency).
Redningsoperationer fortsatte i byen Joso, et af de sværest ramte områder, selvom vandmasserne er på retur, tilføjede den.
I alt er 2,8 millioner mennesker blevet rådet til at evakuere, sagde redningstjenesten.
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Rescue teams in the Miyagi city of Osaki battled to save residents Friday after a section of a levee containing the Shibui River broke.
In some areas during the past two days, residents were forced to their rooftops, desperately awaiting rescue by military helicopters.
The raging brown floodwaters spawned from Tropical Storm Etau, which has dumped more than 60 centimeters (2 feet) of rain over some areas since Monday.
Add several weeks of near-daily downpours as the rainy season lingers, and swaths of eastern Japan are now deluged.
"Tochigi Prefecture is facing a grave danger and is in an emergency situation," Japan Meteorological Agency spokesman Takuya Deshimaru said. "It is experiencing unprecedented downpour."
In Joso, Japanese forces helicopters landed on the roof of a shopping center Friday, where dozens of people had been stranded overnight.
In a rare break from the rain, the sun allowed floodwaters to visibly recede, but many roads remain impassable. Drivers who attempted to brave the inundated streets were forced to abandon their vehicles.
Most of those reported missing were in the city.
Joso, Japan
"Our home is a total loss but at least everyone in our family is safe," Hirose said.
His father, Ai Hirose, 85, described it as the worst flooding he's seen in his lifetime along the Kokaigawa River.
In parts of Tochigi, more than 50 centimeters (20 inches) of rain fell in 24 hours, Japanese broadcaster NHK reported. That's about double the amount that typically falls in the region for all of September, it said.
Fukushima prefecture, which was devastated by the 2011 tsunami, saw more than 30 centimeters (1 foot) of rain in 48 hours -- the heaviest downpour there in 50 years, NHK said.
TEPCO, the company that operates the failed reactors in Fukushima where the tsunami caused one of the biggest nuclear accidents in history, said it detected slightly tainted "rainwater flowing out into the ocean" from the site this week.
CNN's Yoko Wakatsuki reported from Japan and Katie Hunt wrote from Hong Kong. CNN's Will Ripley and Euan McKirdy contributed to this report.
Kommentar: Hvor er det meningen at disse 3 millioner mennesker går hen?
Japan er ikke det eneste sted hvor der er naturkatastrofer såsom oversvømmelser, ildebrande, vulkanudbrud og jordskælv. Se vores månedlige resume af disse hændelser som vi kalder jordomvæltninger: