The floods in Sentani, near the provincial capital of Jayapura, were triggered by torrential rain on Saturday, and also left 21 people injured.
Dozens of homes were damaged by floodwaters, national disaster agency spokesman Sutopo Purwo Nugroho said.
"The number of casualties and impact of the disaster will likely increase as search and rescue teams are still trying to reach other affected areas," he added.
The floods have receded, but officials are still trying to evacuate people.
Flooding is not uncommon in Indonesia, especially during the rainy season which runs from October to April.
In January, floods and landslides killed at least 70 people on Sulawesi island, while earlier this month hundreds in West Java province were forced to evacuate when torrential rains triggered severe flooding.