The floods have killed at least 25 people and left about 340,000 homeless.
In some parts of the city, flood waters are up to four metres deep after several rivers burst their banks.
Boats and helicopters have been used to ferry emergency supplies to dozens of residents trapped on the roofs of buildings, unable or unwilling to leave their homes.
Güncelleme Tarihi: 20 Eylül 2018, 18:16
Medical teams have also been sent by boat to the thousands stranded by the floods, amid fears that disease may spread in the contaminated flood waters.
Forecasters say heavy rains are likely to hit the capital area for at least the next two weeks and could raise the floodwaters even further.
"Jakarta is now on the highest alert level," said Sihar Simanjuntak, an official monitoring the water levels of the many rivers that crisscross the capital. "The floods are getting worse."
|Officials say up to three quarters of the |
city has been hit by floods [AFP]
"We fear that diarrhoea and dysentery may break out, as well as illnesses spread by rats," Dr Rustam Pakaya of the Indonesian health ministry said.
"People must be careful not to drink dirty water."
Rescuers said that most of the dead were killed by drowning or electrocution.
According to the government's crisis centre, about 340,000 people have been made homeless, many of them staying with friends, family or in mosques and government buildings.
Many residents escaped their homes on inner tubes, children's inflatable paddling pools and makeshift rafts, or by wading through the floods rather than wait for help to arrive.
The floods have forced city officials to cut off water and power supplied to parts of the capital.
They have also closed several main roads across Jakarta, while at least two hospitals had to move patients to upper floors.
On Sunday, Indonesia's environment minister blamed the city's worst floods in memory on excessive construction on natural drainage areas.
Rachmat Witoelar was quoted by the official Antara news agency as saying many developers had not paid enough attention to the ecological impact of their construction projects.
But Jakarta's governor rejected the suggestion, saying the heavy rains were a "cyclical natural phenomenon".