"We didn't have time to carry anything with us except our clothes," Sri, the wife of a building construction worker, told Agence France Presse (AFP).
Nine-month pregnant with her second child, she lamented losing everything they own to the swirling brown waters.
"My marriage certificate and other documents were washed away when we left our home," said Sri.
"We have to start all over again."
Police sources said more than 29 people were killed in the worst floods to hit the tropical capital in five years.
Rescuers said that most of the dead were killed by drowning or electrocution.
"In Jakarta, Bekasi and Tangerang, 340,000 people have been displaced," Rustam Pakaya, a health ministry official, told Reuters by telephone.
Tens of thousands of houses have been inundated after rivers and canals which criss-cross Jakarta burst their banks following days of torrential downpours in the city and the adjoining towns of Tangerang and Bekasi.
The floods are the worst to hit Jakarta since 2002, when 40 people were killed, and meteorologists have predicted the heavy rain will continue.
Boats and helicopters have been used to ferry emergency supplies to residents trapped on the roofs of buildings, unable or unwilling to leave their homes.
"The focus today remains the evacuation of people from flooded areas in Jakarta, Tangerang and Bekasi," said Mursid, an officer in charge at the National Disaster Mitigation Coordinating Centre.
Many residents have escaped their flooded homes on makeshift rafts or by wading through the waist-high muddy and polluted waters rather than wait for help to arrive.
Others remained trapped on the roofs of their houses or were refusing to leave, preferring to stay with their relatives or to guard their belongings despite the lack of drinking water and electricity.
Jakarta governor Sutiyoso appealed to residents to leave their flooded homes for their own safety and to ease the distribution of relief supplies.
"Do not hesitate to leave areas which we deem as being on top alert and which urgently have to be evacuated," he told ElShinta radio.
"If you refuse to be evacuated, it will only endanger yourself and it is also very difficult to push relief door-to-door."
Wealthier residents of the capital headed for the luxury hotels, while poorer people sought refuge wherever they could, even in graveyards.
Hundreds of people were sheltering in the Karet cemetery in the center of town.
"This is the safest place during the regular five-year floods," Barbera Pohan told Jakarta Post as she and her children crouched under makeshift tents.
Members of the Indonesian Red Cross and other volunteers were delivering food to thousands of people camped out on roadsides or in public buildings and mosques turned into temporary shelters.
The Indonesian Red Cross said it was supplying water to some 30,000 people in one North Jakarta ward alone.
Australian ambassador Bill Farmer said 150,000 Australian dollars (117,000 US) donated by his government would provide thousands of emergency food parcels and hygiene kits to be distributed by the Indonesian Red Cross.
"We are in close contact with the Indonesian government and other humanitarian agencies and stand ready to provide further assistance as required," Farmer said in a statement.
The US embassy said it would give 100,000 dollars in emergency assistance through the Red Cross and other organizations to provide emergency supplies and items such as plastic sheets, cooking utensils and sleeping mats.
Indonesian officials said that more than 50,000 residents in Jakarta have sought treatment for conditions ranging from coughs to diarrhea.
Health Minister Siti Fadillah Supari warned that the capital of 9 million residents is on alert for outbreaks of more serious diseases such as typhoid, cholera and measles.
The floods have forced the closures of several main roads across Jakarta, while at least two hospitals had to move patients to upper floors.
Environment Minister Rachmat Witoelar has blamed the floods on excessive construction on natural drainage areas but governor Sutiyoso said it was a "cyclical natural phenomenon."
Old Batavia, the former colonial port under the Dutch from where Jakarta has expanded, was built on marshland and some areas of the capital are below sea level.
Indonesia, the world's most populous Muslim nation, is regularly struck with floods.
The sprawling archipelago of 17,000 islands is afflicted with seasonal downpours cause that usually dozens of landslides and flash floods each year.Güncelleme Tarihi: 20 Eylül 2018, 18:16