Many people had to wait overnight to be rescued from the roofs of their homes near Joso city, after the Kinugawa River burst its banks on Thursday.
Officials have warned of further heavy rain and the risk of mudslides.
An evacuation warning was also issued for 410,000 people in Sendai, capital of Miyagi prefecture, on Friday morning, after the Nanakitagawa River flooded in Izumi ward, swamping homes and fields.
The Shibui River in the mostly rural city of Osaki in Miyagi prefecture, around 350 km (220 miles) north of Tokyo, also burst its banks on Friday morning, inundating rice fields and houses. Rescuers in boats and helicopters are rescuing stranded residents there.
The rainfall comes in the wake of Typhoon Etau, which ploughed through Japan earlier this week.
Some 51 helicopters and nearly 6,000 rescuers worked through the night on Thursday.
Emergency crews in Joso have been plucking dozens of people from rooftops after waiting overnight. They were taken to an athletic field in the city, many carrying almost nothing with them. Some arrived without even shoes.
More than 3,500 people have been taken to temporary shelters during the disaster.
Japan`s public broadcaster NHK said that in Joso alone, nearly 700 people were still stranded and waiting for help on Thursday evening.
Officials in the city of 60,000, about 50km northeast of Tokyo, said 22 people there had lost contact after requesting help. NHK reported that two eight-year-old children were believed to be among them.
Floodwaters had subsided somewhat by dawn on Friday, but much of the city was still under water and it is not clear when evacuees will be able to return home.
Across the affected region, one 63-year-old woman was killed after her house was hit by a landslide in Kanuma City in Tochigi.
A second woman, 48, was killed after her car was swept away in Kurihara city, Miyagi prefecture.
At least 27 people have been injured, eight seriously.
Sixty-two year old Hisako Sekimoto, who was rescued by military helicopter in the early morning, said she spent a sleepless night on the upper floor of her flooded house with her husband and three cats.
"There was no time to escape. All we could do was go upstairs. It was horrifying,`` she said. "I kept praying the water wouldn`t come upstairs."
Akira Motokawa, a Joso city evacuation official, told NHK that rescuers have been unable to keep up with the volume of calls for help.
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