Sutopo Purwo Nugroho, National disaster agency spokesman
"The rain started last night and went on until around 1:00 am this morning," said Lilis Puji Hastuti, a 29-year-old mother of two young children in Sentani.
"Our house was flooded with thick mud ... we immediately grabbed our valuables and ran to a neighbour's (two-storey) house to seek refuge.
"It's hard to get out of the area because many roads are blocked ... I'm worried, sad and scared all at one time," she added.
In Sentani, tents have been set up to take in flood victims and treat the wounded.
Papua shares a border with independent Papua New Guinea on an island just north of Australia.
Flooding is common 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.
The Southeast Asian archipelago of some 17,000 islands is one of the most disaster-prone nations on Earth, straddling the Pacific Ring of Fire, where tectonic plates collide.
Earthquakes and volcanic eruptions are common.
"The rain started last night and went on until around 1:00 am this morning. "Our house was flooded with thick mud ... we immediately grabbed our valuables and ran to a neighbour's (two-storey) house to seek refuge
In December, the western part of Java island was slammed by a deadly volcano-triggered tsunami that killed about 400 people.
Also last year, the city of Palu in Sulawesi was rocked by a quake-tsunami disaster that killed thousands, while hundreds of others died in a series of quakes that hit the holiday island of Lombok, next to Bali.