A state of emergency has been declared in the Indonesian capital Jakarta, where three people have died as large swathes of the city grapples with unprecedented flooding.

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.

Residents have been stranded in various parts of the city so military trucks, rescue boats and the police are ferrying people back and forth.

The city's governor Joko Widodo has declared it in a state of emergency until January 27, because the heavy monsoonal downpours are expected to continue until at least then.

Disaster management authorities are struggling to keep track of how many people are now homeless, but it is in the tens of thousands.

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.

Three people have died 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.

NDMC spokesman Sutopo Purwo Nugroho said a child was among the two victims swept away in the floods on Wednesday night.

"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.

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 went 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