The disaster mitigation agency says more than 50 areas are flooded in Jakarta with waters up to 1.5 meters (4.9 feet) high in East Jakarta.
It said the city's drains couldn't accommodate the runoff and rivers also overflowed.
Floods in 2013 forced killed more than two dozen people in Jakarta and forced tens of thousands to flee their homes.
The city, which has about 30 million people in its greater metropolitan area, says it has reduced the number of flood prone areas since then by dredging rivers and other measures.
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