Rescue workers found the body of a person who had gone missing in Chiba prefecture after getting caught up in floodwaters while driving. Another person was unaccounted for in Fukushima, farther north, which is still reeling from damage by Typhoon Hagibis earlier this month.
The death toll from the flooding included nine people in Chiba and one in Fukushima.
While rains and floodwaters subsided, parts of Chiba were still inundated. About 4,700 homes were out of running water and some train services were delayed or suspended.
In Midori district in Chiba, mudslides crushed three houses, killing three people who were buried underneath them. Another mudslide hit a house in nearby Ichihara city, killing a woman. In Nagara and Chonan towns, four people drowned when their vehicles were submerged.
"There was enormous noise and impact, 'boom' like an earthquake, so I went outside. Then look what happened. I was terrified," said a Midori resident who lives near a crushed home. "Rain was even more intense than the typhoons."
In Fukushima, a woman was found dead in a park in Soma city after a report that a car was washed away. A passenger was still missing.
Rain also washed out Friday's second round of the PGA Tour's first tournament held in Japan, the Zozo Championship in Inzai city. Saturday's second round allowed no spectators.
Prime Minister Shinzo Abe held an emergency task force meeting Saturday morning and called for "the utmost effort in rescue and relief operations." He also urged quicks repairs of electricity, water and other essential services to help restore the lives of the disaster-hit residents.
The Prime Minister's Office said the average rainfall for the entire month had fallen in just half a day Friday.
The downpour came from a low-pressure system above Japan's main island of Honshu that moved northward later Friday. Power was restored Saturday at most of the 6,000 Chiba households that had lost electricity. About 390 people remained at shelters Saturday afternoon.
Two weeks ago, Typhoon Hagibis caused widespread flooding and left more than 80 people dead or presumed dead across Japan. An earlier typhoon in September had devastated Chiba, where more than 50,000 homes were damaged or destroyed, and 100 others flooded. Friday's downpour flooded more than 150 homes and damaged several others.
Yoshiki Takeuchi, an office worker who lives in a riverside house in Chiba's Sodegaura city, said he had just finished temporary repairs to his roof after tiles were blown off by the September typhoon when Friday's rains hit hard.
"I wasn't ready for another disaster like this. I've had enough of this, and I need a break," he told Kyodo News agency.