Evacuation orders and advisories have been issued to 460,000 people in western and central Japan, Kyodo News agency reported.
NHK TV footage showed a bridge that had been swept away after intense rainfall, which caused a river to swell with brown torrents. People holding umbrellas waded through knee-deep water in city streets and residential areas.
The center of the season's 12th typhoon was moving slowly north across the Sea of Japan, the Japan Meteorological Agency said. It crossed the southern Japanese island of Shikoku and the central part of the main island of Honshu overnight Sunday.
Because of the storm's slow speed, the agency warned that heavy rains and strong winds are likely to continue and could lead to flooding and landslides.
Three homes were buried in a landslide in Wakayama prefecture, and one woman, who was rescued, whose identity was still being confirmed later died, four remained missing and a 14-year old girl was saved from the debris, police said.
Overall in the hard-hit prefecture, 10 people were dead and 32 people were missing, they said.
Seven people were reported missing in nearby Nara Prefecture, after homes were swept down a river, NHK said.
Among the dead was a woman, who appeared to be in her 30s, whose body was found in a river in Ehime prefecture on Shikoku, police said.
A 73-year-old man in Nara prefecture died after a landslide caused his house to collapse, police said.