Massive floods since last week has killed 50 people, most due to drowning or electrocution, Rustam Pakaya, from the health ministry's crisis centre, said.
Many residents in the Indonesian capital of 12 million people have returned home to clean up their houses and dry out belongings.
"The water is all gone, but the smell is awful," said Fifa, 18, who was cleaning out her house.
"But at least we can get back to normal now," she said.
Many city roads previously submerged in floodwaters have been reopened.
Flood victims who sought shelter at schools, mosques and government buildings have appealed for basic supplies.
Alamsyah, a district official, said: "There is a shortage of baby food and blankets. We need more supplies."
Paskah Suzzeta, the planning minister, said the floods had cost Jakarta an estimated half-a-billion dollars in losses.
The European Union has pledged $777,300 for food, water and sanitation supplies while the Netherlands, Indonesia's former colonial ruler, has pledged $1.3 m in aid.
Flood waters are receding but many areas are still under water