Indonesian disaster authorities have lost count of the number of people who have been left homeless in widespread flooding, but say it could reach the hundreds of thousands.

The centre of Jakarta, including the Presidential Palace, is awash and parts of the Indonesian capital that have never seen flooding before are now underwater.

Yesterday 10,000 people had to flee their homes but hours of heavy downpours overnight and rivers bursting their banks, have added to the problem.

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Three people have been killed so far in the seasonal chaos and the National Disaster Management Centre says it could affect as many as 350,000 as it did six years ago.

"My home is destroyed - all of it. It's in chaotic piles of mess," resident Umar Dani said through a translator.

He said the flood reached the roof of his house.

The National Disaster Management Centre spokesman Sutopo Purwo Nugroho said a child was among the two victims swept away in the floods overnight.

"Days of heavy downpours caused the rivers to overflow and triggered floods up to three metres," he said through a translator, adding that rivers in Jakarta had a low capacity to contain the monsoonal rain.

In 2007, major floods forced 350,000 people to leave their homes and authorities are preparing for the same impact this year.

However, they say it is hard to predict how bad things will get.

Mr Nugroho says the 2007 floods caused nearly $500 million of damage in Jakarta alone.

"It's serious because this is the capital of Indonesia and flooding can affect the economy locally and nationally," he said.

Indonesia is regularly afflicted by deadly floods and landslides during its wet season, which lasts around half the year, and many in the capital live beside rivers that periodically overflow.

At least 11 people were killed and seven missing in November after flash floods triggered by heavy rain hit a village on Indonesia's Sulawesi island.

There is more than two months of the wet season to go.

ABC/AFP