More than a dozen people were missing after the rain hit the province of Bengkulu, on the southwest side of Sumatra, on Friday and Saturday, the agency said.
Hundreds of buildings had been damaged, along with roads and bridges, with two districts cut off by landslides, adding that the floodwater had subsided in some places.
Displaced villagers needed tents, boats, food and water, while heavy equipment was also needed to build temporary bridges.Authorities have warned of the risk of disease spreading due to the lack of clean water.