There were no immediate reports of casualties after the latest deluge, but parts of the city, home to around 11 million people, ground to a halt as whole neighbourhoods were swamped in muddy water.
Heavy rain began on Monday, causing some flooding in Jakarta and nearby the cities of Bogor, Bekasi and Tangerang.
Water was seen metres high in areas of east and south Jakarta on Tuesday after the rain caused the Ciliwung river to overflow, affecting 1,446 people from 224 houses in one village alone, the National Disaster Mitigation Agency (BNPB) said.
In Bogor, more than 300 people were evacuated, dozens of houses were damaged and one bridge collapsed. In Tangerang, 350 houses were flooded after the Cimanceuri River overflowed.
Residents took to rooftops or used ropes to pull themselves to safety through the floodwater in one south Jakarta district, according to an AFP journalist at the scene.
Authorities said they were distributing ready-to-eat food, blankets and tarpaulins to those affected by the floods, and deploying rubber boats to evacuate residents.
"If there is a shortage, the public can ask for more. We are ready to help," BNPB deputy for emergency response Lukmansyah said in a statement.
The low-lying city is prone to flooding during the wet season which runs from around November to March.
In 2020 torrential rain triggered flooding and landslides that killed nearly 70 people in and around Jakarta, while thousands more were forced to evacuate to shelters.
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