JAKARTA: Floods in Indonesia's capital Jakarta have left at least 11 people dead, authorities said Friday as murky brown waters submerged parts of the city's business district, causing chaos for a second day.

The capital's worst floods in five years have also forced 18,000 people from their homes, the nation's disaster agency said, with many ferried to temporary shelters on rafts.

“Floods are occurring still and since Jan 15, 11 people have died, five of which from electrocution,” said National Disaster Mitigation Agency spokesman Sutopo Purwo Nugroho.

Among the dead were two children aged two and 13, said Nugroho, adding that although waters were receding eight per cent of the capital was still inundated and a city-wide state of emergency would apply until Jan 27.

The flooding caused chaos in Jakarta's upmarket downtown district, causing hours-long traffic jams as motorists struggled to get to work along canal-like streets.

Drivers could be seen standing miserably in raincoats, waiting for their flooded cars to be towed away. Other vehicles lay abandoned by the side of the road.

At the landmark Hotel Indonesia traffic circle, surrounded by office towers, five-star hotels and shopping centres, the brown floodwaters continued to swirl, forcing the nearby British, German and French embassies to remain shut.

The central business district normally escapes damage in the Indonesia's monsoonal rains but it was hit by waist-high water Thursday, forcing some commuters to wade their way to work holding bags aloft.

Jakarta, home to 20 million people, is notorious for its traffic-clogged streets, but the floods brought a new dimension to the commute.

“It took me two hours to get to work,” said Shinta Maharani, whose home is just seven kilometres from her office.

“I had to abandon the motorbike taxi and walk for 40 minutes because the road ahead was submerged.”

Many train and bus routes serving the city centre were also suspended.

“The government is trying to keep doing emergency mitigation efforts,” the disaster agency spokesman said.

The floods were the worst to hit the capital since 2007, when about 50 people were killed and more than 300,000 were displaced.

Even the presidential palace was inundated by the waters, with President Susilo Bambang Yudhoyono pictured in the grounds Thursday in rolled-up trousers as he ordered officials to ensure public safety.

Authorities raised the flood alert to its highest level Thursday, warning that the torrential rains would not subside until the end of the week.

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 which periodically overflow.