Fourteen victims were found in the same flooded nursing home while the other was pulled from a landslide. The deaths have yet to be formally certified.
The authorities have ordered more than 200,000 to evacuate and 10,000 soldiers are being sent to help rescuers.
Heavy rain is predicted to continue overnight into Sunday.
Prime Minister Shinzo Abe urged people to be on "maximum alert".
The prefectures of Kumamoto and Kagoshima have been worst hit.