Authorities said half of Manila had been hit by floods, with water up to waist and neck levels in some areas.
There were no new reports of casualties from these floods.
More than 50 people died after Typhoon Saola struck over a week ago, mostly in the north of the country.
The severity of the rain since Monday afternoon – in an already saturated city – has led officials to issue the highest level of alert.
Weather officials warn that the floods could get worse as the overflowing La Mesa dam, which holds back Manila’s main reservoir, spills more water.
“If we put it in a percentage, at least 50% of Metro Manila is flooded,” Jean Navarez, from the state weather service, was quoted by Agence-France Presse news agency as saying.
“There will be heavy rainfall for the next 24 hours. The floods will increase.”
For many Manila residents, these rains will be a reminder of the deadly floods caused by Typhoon Ketsana in 2009, which killed more than 400 people.
Residents living in slums and shanty-towns on low ground have taken shelter in community buildings.
Several key roads were impassable and power had also been cut in some areas, mostly as a precaution, officials said.
Rescue efforts are now underway to help stranded residents.
“As of now, it’s difficult to rescue the trapped residents, as we are battling strong currents with our life crafts,” police rescuer Eric Baran told Reuters news agency.
Sustained rains from Typhoon Saola have forced hundreds of thousands to leave their homes across the country, according to officials from the National Disaster Risk Reduction and Management Council.
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