Dozens of residents in parts of the capital's east, where flooding occurs frequently during rainy season, were forced to wade through streets filled with water 1m deep.
Images from some parts of the city showed people taking refuge on higher grounds with their belongings, while the authorities tried to reach hard-hit areas with rubber boats.
Public kitchens have been set up in the east of Jakarta to distribute aid to people affected by the flooding.
The agency warned that water at several dams is still at a worrying level.
There are no immediate reports of deaths or injuries, it said.
The local media reported on April 24 that at least four people were killed and two others reported missing after heavy rain triggered flash floods in central Java.
Last month, at least 104 people died and over 10,000 others were forced to evacuate after flash flood and landslides tore through Papua in eastern Indonesia.
Flooding is common in Indonesia, especially during the rainy season that runs from October to April.
