The floods, triggered by heavy rain on Saturday, hit two separate parts of Nduga regency in the eastern province of Papua Pegunungan.
After initially announcing that 23 people were missing, Abdul Muhari, spokesman for the disaster management agency, said that "15 people have been found dead."
He said that the search was ongoing for the remaining eight.
Massive landslides in the area have hampered the operation, Abdul said in an earlier update.
He had also said that those missing included 15 people who were swept away by a flash flood while attempting to cross a river, but it was not immediately clear whether this was the group that was eventually found dead.
The annual monsoon season in Indonesia, typically between November and April, often brings landslides, flash floods and water-borne diseases.
Climate change has affected storm patterns, including the length and severity of the season, leading to heavier rain, flash flooding and stronger wind gusts.
At least 18 people died in September when a flood hit Bali -- the popular holiday island's worst in a decade, according to the Meteorology, Climatology and Geophysics Agency.
In January, floods and landslides in Central Java province killed at least 25 people.