Aerial footage showed emergency workers removing wreckage from two houses that were swept away in Chiba, southeast of Tokyo, just two weeks after a deadly typhoon barrelled through the area.
Nine people were killed by landslides and floods in the region, including two elderly men found dead in submerged cars, officials and news reports said.
A woman in her 40s was found dead near the coast in eastern Fukushima, according to a fire department official.
Police divers were deployed to search for those unaccounted for, with public broadcaster NHK putting the number of missing at three.
Thousands of people were forced to spend the night in Narita airport after train services were suspended, it added.
"Water was flowing in my garden like a river," a 75-year-old man told NHK. "Rain was heavier than during the typhoon."
Two weeks ago, Typhoon Hagibis slammed into the east coast of Japan, killing more than 80 people. Many river banks and levees that were breached during Hagibis have yet to be repaired.
The rescue effort received some relief when the Japan Meteorological Agency downgraded warnings of landslides and floods as rains eased on Saturday morning in many regions.
Non-mandatory evacuation orders were also lifted in many areas, although 1,800 people were still in shelters, NHK reported.