Health officials in the city of Iligan say unclaimed bodies are being buried after being marked for possible future identification.
Coastal communities were devastated early on Saturday in flash floods triggered by a tropical storm.
More than 650 people were killed and another 800 people are still missing.
Damaged roads are hampering efforts to reach survivors in remote villages.
Officials in Iligan said they were preparing to bury unclaimed bodies in a mass grave as early as Monday because of their advanced state of decomposition.
The ports of Iligan and nearby Cagayan de Oro bore the brunt of the flooding.
Health officer Liddy Villarin said the body bags would be marked for possible exhumation.
"We will put markings on the cadaver bags which will give the physical features of each body before they put them in the mass grave," she said.Corpses unclaimed
Disaster management chief Benito Ramos said funeral parlours had been overwhelmed by the catastrophe.
Speaking from a boat off Cagayan de Oro, he told AFP news agency: "I'm out here retrieving bodies that are starting to rise to the surface."
The Philippine Red Cross said its staff had confirmed 652 people dead and another 808 were listed as missing.
Officials in Cagayan de Oro said corpses were piling up unclaimed at mortuaries and overworked staff had run out of coffins.
One establishment turned away the bodies of two drowned children, local media reported.
About 35,000 people are sheltering in evacuation centres, the National Disaster Risk Reduction and Management Council said.
The government says survivors are in desperate need of fresh water, shelter and medicine.
China and the US are among international donors offering assistance.
The flash floods struck in the early hours of Saturday as a passing tropical storm coincided with high tides.
As rivers burst their banks, many were trapped in their homes while in other areas entire villages are reported to have been swept away.
Authorities are facing criticism for not giving enough warning of the storm's severity.
BBC
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