Several injured and thousands evacuated as damaging winds and torrential rains lash the island of Honshu.
Thousands of rescue workers have continued to search for more than 20 missing people in a flooded city near Tokyo, a day after a raging river washed away houses and killed at least three people.
Officials in Joso City said on Friday that 22 people remained missing after they had lost contact with them following requests for rescue. Three were injured, including one seriously.
Two eight-year-old children were believed to be among the missing, NHK national television said.
One 63-year-old woman was killed on Thursday after her house was crushed by a landslide and another when her car was swept away.
One man was also pronounced dead after he fell into a ditch in the city of Nikko, Tochigi prefecture.
More than 3,500 people were staying in evacuation centres.
Dozens of residents were airlifted out by military helicopters on Friday morning after waiting overnight in the disaster-struck city north of the Japanese capital.
They arrived at an athletic field in the city, carrying a few clothes and food in shopping bags, some of them without shoes.
Some 300km to the north, another river overflowed into the city of Osaki on Friday, swamping homes and fields and stranding 60 people, according to media reports.
In an interview with Al Jazeera, Rachel Mealy, a journalist in Tokyo, said that as of Friday morning, flooding had subsided, but “the devastation left behind is extreme”.
Helicopters crisscrossed the skies over the largely rural city of Joso City, where the brown waters of the Kinu River inundated rice fields and houses as police officers and Self-Defence Force personnel in rubber boats ferried people to safety.
The government set up an emergency centre, and Prime Minister Shinzo Abe told a meeting of ministers that the “unprecedented” rain had created an emergency.
“The government is putting in the best effort to rescue those who are waiting for help as soon as possible,” Chief Cabinet Secretary Yoshihide Suga told a news conference.
“We are still confirming people’s safety one by one, based on various information right now. No comment regarding the number of missing people,” Suga added.
Some parts of Japan had received more than twice the usual September amount of rain in 48 hours by noon on Thursday, leading to some of the worst flooding in more than 60 years.
Japan has put a heavy emphasis on disaster prevention since a 2011 earthquake and tsunami killed nearly 20,000 people and authorities are keen to avoid the kind of criticism they faced then for what was seen as a sluggish response.