Authorities forecast more heavy rain, as they struggle to help people in flood-devastated areas.
Philippine authorities have warned an approaching storm could bring more heavy rain to the capital and surrounding areas that are still reeling from devastating floods that have left 92 dead.
Nearly half a million people are packed in evacuation centres, while all in all, more than 3.4 million people have been affected by the floods, the National Disaster Risk Reduction and Management Council said on Monday.
Flooding in Manila has largely subsided, although hundreds of thousands remained cut off by neck-deep floods in low-lying farming towns north of the capital that are natural catch basins.
"These are the people we are most worried about," civil defence head Benito Ramos told the AFP news agency.
"We have not yet fully recovered and here comes another storm.
"We will continue with our alert levels until we see the full effects of this approaching weather disturbance."
The state weather bureau confirmed on Monday that a tropical depression was spotted 600 kilometres off the eastern coast of the Philippines in the Pacific Ocean.
It was forecast to move in a west-northwest direction and likely skirt the Philippines, but it could still bring heavy rains by Monday night, the bureau said.
Similar heavy rainfall submerged more than 80 per cent of the capital Manila last week, virtually bringing the megacity to a standstill.
Authorities said they were checking for possible outbreaks of disease and rushing food packs to evacuation centres, while the death toll had meanwhile risen to 92 from 85 reported on Sunday.
Many of the casualties were due to drowning.
The Red Cross put up huge rubber bladder tanks for clean water, while local officials sent portable latrines to packed evacuation centres."We have deployed health officers in evacuation centres and in flood-hit communities with the likelihood of diseases erupting."
The World Food Programme has begun to distribute tonnes of emergency food aid. Food packs were also rushed to about 770,000 people displaced by the floods that submerged about 80 per cent of Manila last week.
Outbreak of disease
More than 441,000 people displaced by the floods are crammed into schools, gymnasiums, churches and other government-run makeshift evacuation centres.
Benito Ramos, the head of the civil defence office, said more than half were living in dire conditions in 948 evacuation centres.
"Many have returned to their homes as the waters subsided, but it is far from a normal situation," Ramos said.
"We are trying to help them return to their normal lives with a massive clean-up operation. There is muck everywhere, and it would take some time."
The health department said water purification tablets were being distributed, while mass immunisations were being carried out to prevent an outbreak of colds, flu and other diseases.
Of particular concern is a possible outbreak of leptospirosis, a bacterial disease caused by exposure to water contaminated by rat urine.
More than 3,300 people were infected and 249 died of the disease in the aftermath of similar flooding in 2009, the biggest casualty figure for leptospirosis in the world, health authorities said.