The floods were triggered by tropical storm Ketsana which hit the capital on Saturday with the heaviest rainfall seen in more than 40 years.
The nine-hour downpour left some areas of metropolitan Manila, a sprawling city of 12 million people, under six metres of water.
The death toll is expected to rise further as clean up efforts begin and forecasters have warned another major storm could hit the country in the next two days.
With more than 435,000 people displaced and large areas still submerged, the government said on Monday that emergency services were struggling to cope and apologised for the delays in rescue efforts.
"We are concentrating on massive relief operations. [But] the system is overwhelmed, local government units are overwhelmed," Anthony Golez, the deputy administrator of the National Disaster Co-ordinating Council (NDCC), told reporters on Monday.
"We were used to helping one city, one or two provinces but now, they were following one after another. Our assets and people are spread too thinly."
Countering the threat of disease outbreaks and providing survivors with aid were among the top concerns, officials said.
However, as the scale of the disaster becomes clearer criticism of the government's handling of the floods has grown, with many callers to talk radio stations saying officials had little idea how to respond.
Ramon Casiple, executive director of the Institute for Political and Electoral Reform, told Reuters, told Reuters news agency the disaster could further sink the popularity of the current administration.
"People are wondering how the government spent its budget for flood control projects," he said.
"The government was caught unprepared."
Loren Legarda, a Philippine senator and a regional advocate for disaster risk reduction, told Al Jazeera that government departments had been "totally incompetent and helpless in dealing with this natural disaster".
"Natural disasters don't have to turn to tragedies if there is a clear disaster risk reduction policy," she said.
|The government said nearly 8,000 people have been rescued so far [Reuters]
"The NDCC was totally unprepared for this. They should have allocated funds for local government units ... to have basic equipment to rescue people - it is not the first time that a typhoon has hit the Philippines.
"We should be proactive and prepared, not reactive," Legarda said, blaming a "lack of political will" for the shortcomings.
But Philippines Defence Secretary Gilbert Teodoro, who also serves as chairman of the NDCC, defended the government response saying recovery efforts were still in their early stages.
He said the magnitude of the resources needed was "immense" and that local and national officials were doing their best to assess where best to deploy recovery teams and materials.
The government, which says more than 7,900 people have been rescued so far, has declared a "state of calamity" in Manila and 25 storm-hit provinces, allowing officials to use emergency funds for relief and rescue.