Health officials have warned of a growing risk of disease from the filthy floodwaters inundating the Indonesian capital, where hundreds of thousands of people have been forced to flee their homes.

Torrential rains have raised water levels still further, bringing more misery to Jakarta and the surrounding area where the floods have already killed at least 36 people.

Officials warned of the risk of leptospirosis, which causes high fever and painful joints, from the contaminated flood waters.

Jakarta's health office deputy head Salimar Salim urged people in flooded areas to take precautions against the bacterial disease which is mainly spread by rat urine and can survive for months in water and on the ground.

"We urge (people), that when they clean up after the flood, to use rubber gloves and rubber boots," the Detikcom news portal quoted him as saying.

So far nearly 40,000 people have been treated for minor ailments, officials said.

"So far we have had a few cases of diarrhoea, cases of respiratory diseases and also skin irritations, but we have so far no report of cases involving dangerous diseases such as tetanus or leptospirosis," said Rustam Pakaya, head of the health ministry's crisis centre.

"As of today (Tuesday), we have distributed 12 tonnes of medicine for Jakarta, West Java and Banten, and deployed over 3,000 medical staff," he told AFP, adding that 200 doctors were helping in flood relief operations.

The state Antara news agency said more than 38,000 people had been treated for various ailments.

Medical aid group International SOS also warned of the risk of disease from the polluted waters.

"Flooding can also lead to gastro-intestinal illness like cholera and typhoid, especially if people consume unsafe food and water. Flood waters are usually polluted with elements like oil and lead as well as disease-causing organisms like the bacterium E. coli," it said in a medical alert.

More than 40,000 police, troops and volunteers were helping to evacuate and bring aid to around 340,000 people displaced by the massive floods.

Jakarta police spokesman Ketut Untung Yoga Ana told journalists the death toll had risen to 36, with one man still missing.

Rescuers were trying to evacuate people who have so far refused to leave their flooded homes, said Eman from the East Jakarta disaster mitigation centre.

Many still refuse to leave, saying they feared for their belongings or that conditions at the shelters were no better.

Heavy downpours have raised the water levels at all of the city's main floodgates and further rain is forecast.

The water level at one sluicegate rose 80 centimetres (32 inches) overnight to 960 centimetres (32 feet), 210 centimetres above normal levels, an official at the public works ministry's crisis centre said.

"It has now descended to 919 centimetres but it can still rise again, depending on whether rains continue to fall in the Bogor area," said Agus, an employee there, referring to the city's water catchment area to the southeast.

Rain is forecast until at least Wednesday.

"Our three-day forecast shows that rains will continue to fall but with less volume than the first five days of this month," meteorology office spokesman Ahmad Zakir said.

Between 12 and 15 centimetres of rain have fallen daily but he said it was now likely to drop to around eight to 10 centimetres.

ElShinta radio reported that flood waters had returned in some areas where they had started to recede and callers from the south and southwest of the city said water levels were rising again in their areas.

Environment Minister Rachmat Witoelar has blamed the floods on excessive construction on natural drainage areas, but city governor Sutiyoso said it was a "cyclical natural phenomenon."

Old Batavia, the former colonial port under Dutch rule from where Jakarta has expanded, was built on marshland and some areas of the capital are below sea level.