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.
Kumamoto's governor, Ikuo Kabashima, told reporters the victims at the nursing home had been found "in cardio-respiratory arrest" - a term used in Japan before a doctor officially certifies death.
Footage shows a bridge over the Kuma river washed away, with other pictures of submerged cars and houses.
Japan's Meteorological Agency said such rainfall had never been seen before in the region.
One woman who sought refuge at an evacuation centre said she had never imagined rain could be so powerful, while another said she could feel the vibrations of the churning water from a nearby river
Haruka Yamada, who lives in Ashikita in Kumamoto prefecture, told Kyodo: "I saw large trees and parts of houses being washed away and heard them crashing into something. The air is filled with the smell of leaking gas and sewage."
The NHK broadcaster says there are reports that eight homes in the town's Takinoue district were washed away.