Emergency service personnel were searching for five people who were unaccounted-for, China's state-run Xinhua News Agency reported. Dozens of people were injured.
The typhoon smashed windows and caused other property damage, triggered mudslides and dumped more than 19 inches of rain in a 48-hour period, causing rivers to overflow their banks and prompting evacuation orders in parts of western Japan.
The typhoon flooded more than 300 houses across central and western Japan and caused blackouts in around 80,000 homes, the disaster management agency reported.
In Japan's ancient capital of Kyoto, a popular tourist destination, the Katsura River overflowed its banks, causing major flooding and prompting the evacuation of about 268,000 people, Xinhua said.
Among the flooded sites in Kyoto was Arashiyama, home to a Buddhist temple listed as a World Heritage site. After inspecting Arashiyama Tuesday, Kyoto Gov. Keiji Yamada said the local government would do all it could so the temple could be cleaned and repaired as quickly as possible.
All 81,246 residents of Fukuchiyama were ordered to evacuate, Xinhua said.
Japan's Meteorological Agency said the storm unleashed an "unprecedented amount of rainfall" in Kyoto and two neighboring prefectures.
Transportation across the country was severely hampered Monday but was returning to normal on Tuesday, officials said.