Tropical storm Talas made landfall on the island of Shikoku in western Japan at about 10am local time on Saturday, packing gusts of up to 68mph, Fox News reports.
It was moving north at a slow pace, Japan's Meteorological Agency said.
TV footage showed homes being flooded and large waves pounding harbors, Reuters reports.
Local media reported that five people were missing with about 40 injured.
Kyodo News agency said 3,200 people were evacuated in 16 prefectures, Associated Press reports.
The Meteorological Agency expects the storm to finish passing through Japan early on Sunday and continue heading north into the Sea of Japan.
Tokyo experienced heavy winds but only sporadic rainfall.
The body of a woman believed to be in her thirties was recovered from a swelling river in Tokushima, a major city on Shikoku, a local police spokesman said by telephone, Fox News reports.
More than 300 houses were flooded while several landslides were reported, the National Police Agency said.
The meteorological agency has issued a warning of floods and landslides to residents in western Japan, where heavy rainfall was already reported.