Indonesian soldiers and health workers have sprayed Jakarta with disinfectant to fend off possible diseases that could spread in massive floodwaters that have pooled around the capital.

Key points: Dengue, leptospirosis, and other water-borne diseases may be spread by floodwaters

Dengue, leptospirosis, and other water-borne diseases may be spread by floodwaters More than a 1,000 people have sprayed the capital with disinfectant to halt disease

More than a 1,000 people have sprayed the capital with disinfectant to halt disease Nearly 100,000 people are unable to return home since the New Year's Eve deluge

Monsoon rains and rising rivers submerged a dozen districts in the greater Jakarta area from Wednesday after extreme torrential rains hit on New Year's Eve, causing landslides in hilly areas on the outskirts of the capital that buried scores of people.

At least 60 people have been killed while hundreds of thousands of people have been displaced.

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

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More than a thousand soldiers and health workers sprayed disinfectant in hard-hit areas on Sunday to anticipate possible diseases spread by flooding, such as dengue and leptospirosis, a potentially fatal disease spread by rat's urine, said Ridwan Carman, who is in charge of emergency response and recovery for the Indonesian Red Cross.

About 11,000 health workers were deployed to provide medical care for people affected by the flooding, Health Minister Terawan Agus Putranto said in a statement.

He said there had been no recorded cases of leptospirosis, tetanus or serious waterborne diseases.

92,000 people are unable to return home

The rains also triggered devastating landslides. ( AP: Rangga )

In Lebak, a district in neighbouring Banten province, where flash floods and mudslides swept away more than 1,700 houses and destroyed several villages, rescuers were still searching for a 7-year-old boy reportedly dragged away by flash flooding that killed at least nine people, said Zainal Arifin, a local search and rescue agency chief.

He said mudslides that covered much of the area, blackouts and lack of telecommunications were hampering the search efforts.

Indonesian President Joko Widodo was unable to meet survivors in the devastated village of Sukajaya — where the highest number of deaths were reported — as his helicopter was unable to land due to bad weather, the presidential secretariat said in a statement.

The village is in the hardest-hit district of Bogor, where 16 people were killed by flash floods and landslides.

Waters have receded in most parts of greater Jakarta, allowing many residents to return and clean up, but scores of tightly packed settlements close to rivers that often suffer from floods during the rainy season remained inundated or covered in mud and debris.

Tens of thousands of people remained crammed in damp shelters, mostly in western Jakarta and its satellite city of Bekasi.

Government data on Sunday showed that some 92,200 people were still unable to return home as the filthy waters submerged their houses up to 1.5 metres high.

Residents in places free from floodwaters are now tasked with the clean-up. ( AP: Tatan Syuflana )

'It's disgusting here, but we are stuck'

In a cramped and damp emergency shelter at a sports centre in south Jakarta, mothers breast-fed their babies near piles of smelly, wet garbage.

"My baby is not sleeping as the rain comes in, the wind comes in," Yuyun Yuniarti said while holding her 7-month-old baby in a sling.

"It is disgusting here, but we are stuck."

There are fears over the hygiene of floodwaters that haven't receded in Jakarta. ( AP: Dita Alankara )

Ms Yuniarti said food and medicine appeared to be sufficient, with most shelters visited in recent days by authorities and private organisations delivering regular supplies of food.

A temporary clinic was treating patients close to where Ms Yuniarti was sleeping, including many suffering from respiratory illnesses.

Save the Children, an international child rights organisation, expressed its concern about the dire situation for children.

Tens of thousands of Jakartans are taking refuge at temporary shelters. ( AP: Dita Alangkara )

At least six kids have died from the floods and tens of thousands have had to leave their homes in Jakarta.

"We call on all involved to make sure children are kept safe and have a roof over their heads, and food to eat," Dino Satria, Save the Children's humanitarian director in Indonesia, said in a statement.

He said his organisation would provide school kits, tents and hygiene kits to prevent the outbreak of diseases.

Government has begun cloud seeding to prevent downpours

Numerous parts of Jakarta sit within floodplains. ( Twitter: BNPB Indonesia )

Indonesia's Meteorology, Climatology and Geophysics Agency said that more downpours were forecast for the capital in the coming days, and the potential for extreme rainfall would continue until next month across the vast archipelago nation.

The Government started cloud seeding in an attempt to divert rain clouds from reaching greater Jakarta to prevent possible flooding from Friday, the agency said.

On Saturday, 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.

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.

Indonesia is hit by deadly floods each year, and Jakarta, the capital of south-east Asia's largest economy, is not immune.

Jakarta's disaster-prone location prompted the Widodo Government to announce in August it would move Indonesia's capital to the province of East Kalimantan, on Borneo island.