The storm caused landfall on the Izu Peninsula, southwest of Tokyo, leaving destruction in its wake.
The heavy rain destroyed at least 90 flood sets on rivers, overwhelming more than 33,000 homes.
At least 105,000 households have no water, and thousands of homes have no electricity. It is not known how long it will take to again restore these services.
In addition, Japan was bracing for a secondary disaster on Thursday. Heavy rain was forecast to strike already-overwhelmed areas in the coming days. Officials said additional floods could destroy sets along rivers and trigger more landslides.
ILKHA