More than 1,300 residents have been evacuated to temporary shelters, with parts of the capital under four to nine feet (1.2 to 2.7 metres) of water.
Images showed rescuers on rafts battling to evacuate the elderly and children from submerged houses in hard-hit southern and eastern areas of the city, and dozens of cars were seen submerged on waterlogged streets.
National rescue agency spokesman Yusuf Latif said the floods were triggered by extreme downpours.
"The rainfall intensity is very high due to extreme weather in Jakarta and it's been raining since yesterday night," Latif told AFP.
"Our top priority is children as well as infants and the elderly."
No casualties have been reported so far, he added.
Jakarta, a megalopolis that is home to around 30 million people, is frequently hit by floods in the rainy season.
The city saw some of its deadliest flooding in years in January last year after downpours that also triggered landslides.
At least 67 people in Jakarta and nearby cities were killed in that disaster, with the floodwaters reaching the second floor of some buildings after rivers burst their banks.
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