Indonesia's air force has dropped salt flares on storm clouds in an effort to prevent further torrential rain over the capital Jakarta, after deadly floods ravaged the city over the New Year period.

Key points: Cloud-seeding efforts aim to lessen rainfall over the Indonesian capital

Cloud-seeding efforts aim to lessen rainfall over the Indonesian capital Deaths have been caused by electrocution, drowning and hypothermia

Deaths have been caused by electrocution, drowning and hypothermia Almost 400,000 people sought refuge in shelters across Jakarta

Two planes dropped 2.4 tonnes and 800 kilograms of salt, respectively, in an effort to break up clouds before they reach the city, said the country's technological agency, which has spearheaded the "weather modification" effort.

"Please pray for the successful operation of weather modification to mitigate further flood disasters," tweeted the agency's head Hammam Riza.

Flash floods caused cars to be overturned and entire buildings to collapse. ( AP: Achmad Ibrahim )

Doni Monardo, a spokesman for Indonesia's national disaster management agency, said authorities hope the cloud seeding will reduce rainfall intensity by 20 per cent.

Jakarta was hit by flash floods on New Year's day after some of the heaviest rainfall on record.

The official death toll climbed to 46 on Friday, according to the disaster management agency, which warned the number may continue to grow.

"Communities along the rivers who are at risk of being victims of flash floods [need] to evacuate themselves to safer places," Mr Monardo said.

The Indonesian climatological agency has deemed the New Year's floods "one of the most extreme" rainfall events since records began in 1866.

It has predicted continued rainfall until next week.

A number of the deceased amid the disaster were electrocuted, while others drowned, were killed in landslides or died of hypothermia.

Some 397,000 people had sought refuge in shelters, the disaster management agency said.

13 rivers run through Indonesia's capital. ( Reuters: Nova Wahyudi via Antara Foto )

While much of the floodwaters have receded, thousands of people remain in some 270 shelters around greater Jakarta.

"It is feared that eight of the 13 rivers in Jakarta are overflowing and the other five are at risk," said Dino Satria, humanitarian director for Save the Children in Indonesia.

"The high waters might contaminate clean water resources, which could lead to the outbreak of diseases."

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At least 256 schools have been closed due to the floods, either directly affected by the deluge or being used as makeshift shelters.

"The danger is far from over, we fear that in the coming weeks the situation will get worse," Mr Satria said.

A spokesperson for Dompet Dhuafa, a local humanitarian agency, told the ABC that the main challenge of rescuing people from flooded homes had been that many live in areas with narrow streets, making it difficult for large rescue boats to navigate.

President Joko Widodo has said that the priority for disaster response was the safety of Indonesian citizens.

"I ordered all relevant agencies to work together to save the people, and to give peace to the people," he said.

Save the Children has warned of the risk of waterborne diseases. ( Kompas: Lasti Kurnia )

Home to some 30 million people, greater Jakarta is highly vulnerable to floods — worsened by being the fastest-sinking city on Earth.

Since the 1970s, parts of Jakarta have sunk more than four metres, at a rate of up to 25 centimetres a year.

Modelling from researchers at the Bandung Institute of Technology has shown that 95 per cent of northern Jakarta could be underwater by 2050.

The megacity's severe environmental problems have motivated Mr Widodo's Government to relocate Indonesia's capital to Borneo, a plan it announced last year.