"We fear that diarrhoea and dysentery may break out, as well as illnesses spread by rats," one official said.
More than a third of a million people are thought to have fled their homes amid Jakarta's worst floods in years, caused by days of torrential rains.
While floods were said to have receded in some places, more rain is forecast.
The floods have affected much of the city of at least nine million people - with estimates of the flooded area ranging between nearly 40% and 75%.
Apart from those swept away or drowned, a number of people were killed by electrocution, police spokesman Ketut Yoga Ana said.
Officials said the unsanitary conditions could cause an outbreak of disease, with fresh water and electricity services down in many areas.
Eyewitness: Jakarta floods
"We know it's hard for the residents [to use and drink clean water] under the circumstances, but they have to," said Health Minister Siti Fadilah Supari.
A Jakarta health official was quoted by Reuters saying more than 50,000 people had already sought treatment for conditions ranging from coughs to diarrhoea.
The city was already coping with a surge in cases of dengue fever before the floods.
An official also said the flooding would complicate efforts to tackle bird flu, which has killed 63 people in Indonesia in the past few years, making it the country worst hit by the disease.
Holding out
Several days of torrential rain have caused rivers to burst their banks, sending muddy water up to 3m (10ft) deep into homes and businesses.
Hundreds of residents are still holding out on the second floor of their homes, either trapped or unwilling to move, the BBC's Rebecca Henschke in Jakarta says.
Many people are sheltering in schools and mosques.
Medical teams on rubber rafts are working in the worst affected areas, while thousands of soldiers and extra police have been deployed to help with evacuation efforts.
In some parts horse-drawn carts were deployed to rescue people from their homes.
The government is facing renewed criticism that it could have done more to prevent this disaster.
"Obviously the city did not learn anything after the last [heavy floods], in 2002," the Jakarta Post said, accusing administrators of delaying the building of a canal to control flooding.
RECENT INDONESIAN DISASTERS
"The government is awful," said resident Augustina Rusli, who had held out on the upper floor of her house with her 10-month old baby.
"We have a neighbour who is sick with cancer but no one has come to rescue her,"
Jakarta's Governor Sutiyoso brushed off criticism, saying the floods were a "natural phenomenon".
"There is no point in throwing abuse around," he said. "I was up till 0300 this morning trying to handle the refugees."
The floods are said to be the worst to hit Jakarta for five years.
Although the sun was shining on Monday, officials say there is little prospect of an early improvement in the situation.
Meteorologists warn downpours are likely to continue for at least another week, and with heavy rains falling on hilly regions to the south, more flooding is threatened.
"We expect residents to stay alert because water may rise again and very fast," said Sihar Simanjuntak, an official monitoring river levels.
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