Government agencies are struggling to provide aid to the homeless, many of whom are staying with friends or family on higher ground at mosques and government agency buildings.
Some people have attempted to stay in their properties, living on the second floors of their homes and refusing to be relocated by soldiers using rubber dinghies, officials said.
"Fortunately, people here are helping each other," said Yusnizar, a 53-year-old living in a housing estate on Jakarta's western outskirts where some 1,000 houses were awash with one-metre high muddy water. Like many Indonesians, Yusnizar goes by a single name.
Indonesia's meteorological agency is forecasting rain for the next two weeks.