Media reports from Indonesia say the government has begun building 1,000 temporary shelters for the flood victims in the Wasior area of West Papua province.
Earlier this month, flooding claimed 150 lives in the remote area and left more than 10,000 people homeless.
Jakarta has utilised some of the heavy military presence in Papua to help deploy relief.
But Indonesia's disaster response has been hampered in recent days by other large disasters such as the Mt Merapi volcano eruption and the West Sumatra earthquake.
Andreas Harsono of Human Rights Watch Indonesia says there's been criticism of the government over the slow response to the West Papua flooding, even before these other disasters.
"Another criticism has been that the national emergency office in Indonesia is heavily centralised. They have a big office and many resources in Jakarta but they don't have a presence in remote regions like Papua."