Typhoon Roke, which had swept across the Japanese territory from north to south, left nine people dead, the Kyodo news agency said on Thursday.
Eight people are listed as missing.
A total of 1.2 million people were ordered to evacuate. High-speed and metro trains were halted, highways closed and more than 600 flights grounded.
A total of 1,984 houses were inundated, including in the city of Onagawa in the Miyagi Prefecture, which houses a temporary shelter for those displaced in the March tsunami.
Typhoon Roke made landfall on Wednesday afternoon, tracking across the main island of Honshu and halting efforts to bring a crippled nuclear plant in the Fukushima prefecture under control.
There are concerns that torrential rain could force pools of radioactive water at the Fukushima facility to overflow into the sea or groundwater.
