Tens of thousands of evacuees remain crowded into emergency shelters, waiting for floodwaters to recede in and around Indonesia's capital, Jakarta, as the death toll from massive New Year's flooding reached 47, officials said.

Monsoon rains and rising rivers submerged a dozen districts in greater Jakarta and caused landslides in the Bogor and Depok districts on the city's outskirts as well as in neighbouring Lebak, where a dozen people were buried.

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National Disaster Mitigation Agency spokesman Agus Wibowo said the fatalities included people who had drowned or been electrocuted since rivers broke their banks early on Wednesday after extreme torrential rains throughout New Year's Eve.

Three elderly people died of hypothermia.

It was the worst flooding since 2007, when 80 people died over 10 days.

"The waters came very fast, suddenly everything in my house was swept away," said Dian Puspitasari, a mother of two, who looked overwhelmed as she tried to sweep piles of mud out of her home.

Four days after the region of 30 million people was struck by flash floods, waters have receded in many middle-class districts, but conditions remained grim in the narrow riverside alleys where the city's poor people live.

At the peak of the flooding, about 397,000 people sought refuge in shelters across the greater metropolitan area as floodwaters reached levels of 6 metres (19 feet) in some places, Wibowo said.

Data released by his agency showed some 173,000 people were still unable to return home, mostly in the hardest-hit area of Bekasi, a satellite city of Jakarta.

More than 152,000 people remain in 98 adequately supplied emergency shelters in Bekasi, where rivers burst their banks. Much of the city was still submerged in muddy waters up to 2 metres (6.5 feet) high, according to the agency.

Displaced residents sought shelter at a makeshift tent in capital Jakarta on Friday [Ajeng Dinar Ulfiana/Reuters]

Electricity was restored to tens of thousands of residences and businesses as of Saturday.

Jakarta's Halim Perdanakusuma domestic airport reopened Thursday; its runway had been submerged in the flooding.

Head of the Meteorology, Climatology and Geophysics Agency Dwikorita Karnawati said more downpours were forecast for the capital in coming days and the potential for extreme rainfall would continue across Indonesia until next month.

The flooding has highlighted Indonesia's infrastructure problems.

Jakarta is home to 10 million people, or 30 million including those in its greater metropolitan area.

It is prone to earthquakes and flooding and is rapidly sinking due to uncontrolled extraction of groundwater. Congestion is estimated to cost the economy $6.5bn a year.

President Joko Widodo announced in August that the capital would move to a site in sparsely populated East Kalimantan province on Borneo island, known for its rainforests and orangutan population.