Floods in Indonesia's capital Jakarta which have killed at least 11 people and left two missing eased Friday, authorities said, warning however of more torrential rains which could hamper relief efforts.

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.

"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 eight percent of the capital was still inundated on Friday morning and a city-wide state of emergency would apply until January 27.

By afternoon though, floodwaters had receded in central Jakarta and traffic was back to normal.

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.

"Rescuers are still struggling to search for them," 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.

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

"Based on weather forecast, heavy rains will continue pouring down until Saturday," the agency's spokesman Nugroho said.

Authorities rushed against time Friday to fix a dike which collapsed due to floods near one of Jakarta business areas. Two excavators were seen and dozens of military personnel joined efforts to repair it.

The flooding caused chaos in the morning 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.

As the waters receded, the area around the Grand Hyatt and upmarket shopping centres was left 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.

Greater 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.

In one of worst hit areas in East Jakarta, a man in his early forties told AFP that the government's inability to mitigate annual flooding was causing him to lose hope.

"The government can only talk and talk...every year the condition is like this. All of furnitures, all of them in my bedroom, my television are broken," he said in his flooded neighbourhood.

Television footage showed a large monitor lizard and a three-metre long snake moving through the floodwaters in residential areas of the capital.

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.