Floods that have crippled much of Indonesia's capital worsened Tuesday, inundating thousands of homes and buildings, including the presidential palace, and paralyzing transport networks, officials and witnesses said.

Overnight rains caused more rivers to burst their banks in greater Jakarta starting Sunday, sending muddy water up to 5 feet deep into more residential and commercial areas, said Agus Wibowo, the National Disaster Mitigation Agency's spokesman.

Floodwaters entered parts of Indonesia's presidential palace complex Tuesday morning but the situation was brought under control with water pumps, said Bey Machmudin, an official at the Presidential Office.

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The heavy downpour that hit the capital on Sunday had submerged the state-run Cipto Mangunkusumo hospital, the country's largest hospital, damaging medical machines and equipment, Wibowo said.

Wibowo said the floods on Tuesday inundated scores of districts and left more than 300 people homeless, forced authorities to cut off electricity and paralyzed transportation, including commuter lines, as floodwaters reached as high as 5 feet in places.

Television footage showed soldiers and rescuers in rubber boats struggling to evacuate children and the elderly who were holding out on the roofs of their squalid houses.

Indonesia's meteorological agency is predicting rain for the next two weeks.

The flooding has highlighted Indonesia's infrastructure problems.

INDONESIA FLOODS TRIGGERED BY TORRENTIAL RAIN KILL 17, DISPLACE THOUSANDS

Jakarta is home to 10 million people, with a total of 30 million in its greater metropolitan area. It is prone to earthquakes and flooding and is rapidly sinking due to uncontrolled extraction of groundwater. Congestion is also estimated to cost the economy $6.5 billion a year.

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

Severe flooding and landslides that hit greater Jakarta early last month killed more than 60 people, displaced hundreds of thousands and forced an airport to close.

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Jakarta Gov. Anies Baswedan, who was criticized when massive floods struck the city last month, blamed widespread deforestation in the southern hills, saying it had destroyed water catchment areas.

Seasonal downpours cause dozens of landslides and flash floods each year in Indonesia, a sprawling archipelago of 17,000 islands where millions of people live in mountainous areas or near fertile plains.