Nearly 6,000 Jakartans were forced to leave their inundated homes on Tuesday, following incessant rainfall the previous night.
Authorities predict the capital will experience the peak of the rainy season on Thursday and Friday.
The National Disaster Mitigation Agency (BNPB) reported that at least 5,986 residents had to evacuate to 14 different shelters, while a total of 15,517 residents in 33 districts were affected by floods.
The BNPB has established 28 tactical posts across Jakarta tasked with evacuation and logistics distribution, spokesman Sutopo Purwo Nugroho said.
West Jakarta saw the highest number of evacuees, with 1,660 residents relocated to temporary shelters during the flooding, according to the Jakarta Disaster Mitigation Agency (BPBD).
However, many of the evacuees left the temporary shelters in the afternoon as the rain stopped and floodwater started to recede in some areas.
"Most evacuees have left the temporary shelters. Only some - mostly the elderly - remain," East Cengkareng subdistrict leader AgusMulyadi told The Jakarta Post on Tuesday, adding that at least 1,000 of his residents had evacuated to nearby shelters.
Agus said temporary shelters in his subdistrict would be on standby to anticipate more floods. He said 14 out of 17 community units in his subdistrict were inundated by floodwater up to 1.5 meters deep in the morning, but the water receded halfway by the afternoon.
BPBD Jakarta head DennyWahyu claimed the number of areas affected by the floods was lower compared to last year.
"Last year, 634 community units were affected. Now the figure is 307," he said.