Etau hit western Japan on Friday. Packing gusts of up to 144 kilometers per hour,
Nine people are confirmed by emergency services dead and 12 missing after high winds and pounding rain lashed the country for three days.
One of the worst hit areas was the northernmost main island of Hokkaido, where rain caused extensive damage to homes and transport networks.
Two vehicles, including a van carrying a family of five, were swept away by flood water in the town of Kamishihoro after a bridge was destroyed.
One body was found in the van and the other four people were missing.
According to Kyodo news agency, 85 people were injured in the storm which also flooded around 1,000 houses.
Three day storm
Typhoon the storm system cut across Japan's main island of Honshu, the Meteorological Agency said.
More than 4,600 other people were evacuated due to numerous landslides.
The typhoon also forced the cancellation of domestic flights, ferry services and train runs, press reports said.
Local authorities in Minamata on the southern island of Kyushu, where 19 people were killed in landslides triggered by torrential rain last month, issued an evacuation recommendation to about 3,000 people for fear of further mudslides.