Iwaizumi in Iwate prefecture is one of the worst-affected towns where nine people have died after being trapped in a care home when a nearby river overflowed while another 18 residents remained missing.
Another three persons were missing in northern Hokkaido island after being swept away by an overflowing river, including a 28-year-old man whose car fell into a river due to a damaged bridge, EFE news reported.
Local authorities and firefighters were still searching for the missing.
Meanwhile, the Japan Meteorological Agency announced the beginning of another typhoon, Namtheun, near the archipelago.
Read More: Typhoon hits Japan: 9 killed
Namtheun, the 12th typhoon of this year in the Pacific, is currently south of Okinawa and is moving northwest with winds of up to 90 kph.
The storm was expected to reach southern Kyushu island between Saturday and Sunday and cross the southwestern region of the main Japanese island of Honshu, before continuing northward toward China.