More than 1,000 people in east and south Jakarta were evacuated after torrential rain overnight, local media reported, with households along the winding Ciliwung River among the worst affected by the floods.

"If the flood gets bigger, we will have to take refuge elsewhere, but if it remains this high, then I think we will decide not to evacuate," said resident Isti Barokah, whose home was flooded.

"Most of our stuff is already on the second floor."

Wooden homes along the river were partially submerged in muddy brown water. Children played waist-deep in the water in front of their homes.

Fire department officials dressed in red life jackets inspected the affected areas, where they said some elderly residents and small children were evacuated.

The country's meteorology, climatology and geophysical agency (BMKG) had issued heavy rain alerts across populous Java island, Bali and parts of eastern Indonesia.

Indonesia frequently suffers floods and landslides, particularly during the rainy season from November to March.

President Joko Widodo in October warned of the hazardous impact of the La Nina weather pattern, like flooding, landslides and agriculture losses, after BMKG indicated monthly rain volume could increase by 20 percent-40 percent above normal levels.

The flooding came days after a factory manufacturing batik, a traditional method of creating dyed material and fabrics, was inundated, flooding a nearby village and producing surreal, blood-red waters.

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