According to Japan's Meteorological Agency, in Honshu island's Hyogo prefecture, a 71-year-old man died after sustaining head injuries and the body of an 85-year-old man was also found, Xinhua news agency reported.
Over 4,000 residents in Kochi prefecture on Shikoku island were urged to evacuate in case of landslides and flooding triggered by the powerful typhoon.
The typhoon landed in Kochi prefecture late Thursday, packing winds of up to 180 km per hour and causing heavy rain.
It later headed north and made the second landfall on Friday morning in Honshu island.
Railway services were either cancelled or suspended in Japan. Airline services were also severely affected.