Disaster management officials are readying for more flooding in the capital after heavy rains in Jakarta and upstream in Bogor.
The National Disaster Mitigation Centre's Sutopo Purwo Nugroho says water levels in the dam at Bogor were higher last night than they were before January's big flood, which affected 250,000 people.
Water is due to hit low-lying areas of the capital, forcing thousands from their homes.
Whether the city centre floods again is dependent on the canal floodwalls holding.
A main canal burst its banks in January, swamping the CBD for the first time on record.
If the canal walls hold this time the business district may be spared, but people living in low-lying and poorer areas of the city have little defence against the mass of water heading their way.