More than 4,500 houses and 500 shops in the coastal town of Tebing Tinggi on Sumatra island have been inundated since Saturday, when the Padang and Bahilang rivers swelled after days of torrential rain, said National Disaster Management Agency spokesman Sutopo Purwo Nugroho.
"The floodwater inside people's homes reached one metre (3.3 feet)," Nugroho said, adding more flooding was expected.
Some 17,648 people have taken shelter in tents provided by the government as well as neighbours' homes, Nugroho said, adding there were no casualties.
Environmentalists blame logging and a failure to reforest denuded land in the world's fourth-most populous country for exacerbating the flooding.