The deluge that began on Monday hit Jakarta, home to around 11 million people, as well as the neighbouring satellite cities of Bogor, Bekasi and Tangerang.
At least one person -- who local media identified as a three-year-old girl -- died after torrential rain made several rivers overflow, pushing waters up three metres (9.8 feet) and submerging more than 1,000 homes.
Authorities estimated the bad weather could last until March 11 so took the pre-emptive measure of cloud seeding, prompting rain away from flood-hit areas or drawing rain from smaller clouds to prevent heavier rainfall later.
"Hopefully, with the weather modification, we can reduce it," Dwikorita Karnawati, head of Indonesia's weather agency, told reporters late Tuesday.
"We can't prevent the rain -- that's impossible -- but we can reduce the intensity."
Cloud seeding -- the practice of using planes to fire salt or other chemicals into clouds to induce rain -- will last until Saturday and focus on mountainous areas in West Java province where heavy rainfall can flow down to nearby cities including Jakarta.
"We can't let the clouds get too big, so we will make it come down little by little," said Dwikorita.
Authorities said as of late Tuesday at least 2,200 residents had been displaced by the floods, as locals took to rooftops or used ropes to pull themselves to safety from the high waters.
Rescuers deployed rubber boats and aid to the worst-hit areas to evacuate residents or help those who refused to leave their homes.
The low-lying city is prone to flooding during the wet season, which runs from around November to March.
In 2020, torrential rain triggered flooding and landslides that killed nearly 70 people in and around Jakarta, while thousands more were forced to evacuate to shelters.
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