Floods in Indonesia's capital Jakarta have left at least 11 people dead and two missing, 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 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 January 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 percent of the capital was still inundated and a city-wide state of emergency would apply until January 27.

Jakarta police spokesman Rikwanto, who goes by one name, said that two men had been trapped since Thursday morning in a flooded parking lot in the capital's business district.

"According to their colleagues who managed to escape, when the waters came, the two men did not take it seriously and stayed in the basement until waters came suddenly and submerged the whole basement," he told AFP.

"Rescuers are still struggling to search for them. We started this morning pumping the waters out of the flooded basement," he said, adding that 2,781 police had been deployed to help assist victims from the floods.

At least four scuba divers were also helping to locate the missing, according to an AFP correspondent.

The flooding caused chaos in Jakarta's upmarket downtown district, causing hours-long traffic jams as motorists struggled to get to work. 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 and five-star hotels, the brown floodwaters continued to swirl, forcing the nearby British, German and French embassies to remain shut.

By afternoon though, much of the waters had receded, leaving the area around the Grand Hyatt and upmarket shopping centres caked in mud.

A spokeswoman for the Mandarin Oriental said that despite the flooding, the hotel had seen a surge in demand for rooms from well-to-do clientele prevented from going home by the waters.

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 (four miles) 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 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 on Thursday, with President Susilo Bambang Yudhoyono pictured in the grounds in rolled-up trousers.

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.