Tens of thousands of Indonesians were still unable to return to their waterlogged homes Saturday after flooding hit the Jakarta capital region, killing at least 53 people, authorities said.

More than 170,000 people took refuge in shelters across the massive urban conglomeration -- home to some 30 million -- after whole neighbourhoods were submerged.

Torrential rains that started on New Year's Eve unleashed flash floods and landslides in the region and neighbouring Lebak at the south end of Java island.

On Saturday, Indonesia's disaster agency said the death toll had climbed to 53 with one person still missing.

"We've discovered more dead bodies," said National Disaster Mitigation Agency spokesman Agus Wibowo.

Officials would be visiting the homeless Saturday in the hardest-hit areas, he added.

Shelters filled up with refugees, including infants, resting on thin mats as food and drinking water ran low.

Some had been reduced to using floodwaters to clean themselves and dishes.

"We badly need clean water in this shelter," Trima Kanti said from one refuge in Jakarta's western edges.

"We're cleaning ourselves in a nearby church but the timing has been limited since it uses an electric generator for power," the 39-year-old added.

In hard-hit Bekasi, on the eastern outskirts of Jakarta, swampy streets were littered with debris and crushed cars lying on top of each other -- with waterline marks reaching as high as the second floors of buildings.

The government said Friday it would start cloud seeding to the west of the capital -- inducing rain using chemicals sprayed from planes -- to prevent approaching rainfall from pounding the region.

Waters had receded in many areas and power was being restored after being cut off in hundreds of districts.

The health ministry has said it deployed some 11,000 health workers and soldiers to distribute medicine, disinfectant hygiene kits and food in a bid to stave off outbreaks of Hepatitis A, mosquito-borne Dengue fever and other illnesses, including infections linked to contact with dead animals.

Around Jakarta, a family -- including a four- and nine-year-old -- died of suspected gas poisoning from a portable power generator, while an eight-year-old boy was killed in a landslide.

Others died from drowning or hypothermia, while one 16-year-old boy was electrocuted by a power line.

Jakarta is regularly hit by floods during the rainy season, which started in late November.

But this week's disaster marked Jakarta's worst flooding since 2013 when dozens were killed after the city was inundated by monsoon rains.

Urban planning experts said the disaster was partly due to record rainfall. But Jakarta's myriad infrastructure problems, including poor drainage and rampant overdevelopment, worsened the situation, they said.

Indonesian President Joko Widodo has announced a plan to move the country's capital to Borneo island to take pressure off Jakarta, which suffers from some of the world's worst traffic jams and is fast sinking due to excessive groundwater extraction.