A severe rain warning remained in effect for parts of northern Japan but floodwaters were slowly retreating in the worst-hit city of Joso after toppling trees and washing houses away, sometimes with their owners still inside.
Three people died, including a 63-year-old woman killed after her house was crushed by a landslide and another when her car was swept away. At least 28 people were injured, eight seriously.
Two eight-year-old children were among the missing as the flooding spread north to Miyagi prefecture, whose coastline was ravaged by the March 2011 earthquake and tsunami that left nearly 20,000 dead.
Some of those rescued on Friday said the flooding brought back memories of the lessons learned in that disaster.
"March 11 was the same. The people who didn't run saying that a tsunami would never come faced death," one man said. "Of course, this situation is not as bad, but you have to be responsible for your own life."
A military helicopter arrives before landing on the roof of a flooded shopping center to rescue people in Joso city. - AFP Photo/Kazuhiro Nogi
Helicopters crisscrossed skies over the largely rural city of Osaki, 350 km (220 miles) north of Tokyo, where the brown waters of the Shibui river inundated rice fields and houses as rescuers in rubber boats ferried people to safety.
Others awaiting rescue waved towels from the second floor of flooded houses or peered terrified down at the water.
"My house is done for," one elderly woman told national broadcaster NHK.
At least 30 bags filled with grass and other materials removed in the clean-up of contaminated fields in a village near the destroyed Fukushima nuclear plant were washed away from where they were stored, but most were recovered undamaged and none of their contents had leaked, Kyodo news agency reported.
Some parts of Japan had received more than twice the usual September amount of rain in 48 hours by noon on Thursday, sparking some of the worst flooding in more than 60 years.
Japan has increased emphasis on disaster mitigation since the 2011 disaster and authorities are keen to avoid the kind of criticism leveled at governments in the past for what was seen as a sluggish response.
"We are doing everything in our power to rescue those in need as soon as possible," chief cabinet secretary Yoshihide Suga told a news conference.
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