Reports say nearly 10 000 people have moved to shelters while at least 104 victims are confirmed to have died and 79 are unaccounted for in the aftermath of the disaster, which was triggered by heavy rain on Saturday.
Officials said scores have suffered injuries, including cuts and broken bones, while some 40 unidentified bodies would be buried in a mass grave on Thursday.
Many survivors fear more floods will rip through hard-hit Papua, which shares a border with Papua New Guinea.
“The increasing number of evacuees has made the shelters very crowded and uncomfortable,” said National Disaster Agency spokesman Sutopo Purwo Nugroho.
As teams loaded mud-caked corpses into body bags, the search for survivors was hampered by mountains of debris including rocks and fallen trees.
Hundreds of homes, bridges, schools and other public facilities were destroyed.
More than 2 300 personnel have been deployed to search for the missing victims and to clean up debris.
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.