Philippine authorities on Tuesday began burying the dead from flash floods that have left more than 1,000 dead or missing, as President Benigno Aquino declared a national disaster.

Aquino flew to Mindanao island to inspect the ports of Cagayan de Oro and Iligan -- choked with drying mud, crumpled homes, and hundreds of decomposing corpses after being struck by tropical storm Washi on the weekend.

Two dump trucks arrived at the public cemetery in Iligan at dusk, with soldiers unloading 38 coffins of victims who have been identified and claimed by relatives, who cried and lit candles as they witnessed the burial.

On Monday as the stench of rotting bodies grew unbearable and health fears rose, local authorities had announced plans for burials in mass graves but after intense criticism they hastily arranged individual tombs.

"It is not like digging a hole and sticking them in there. They are being given apartment-style compartments, and I think it's pretty decent," Iligan city Mayor Lawrence Cruz told AFP as he led the first of the burials.

A priest sprinkled holy water on each coffin before it was pushed into the tombs.

Cruz said that forensics experts were taking fingerprints and DNA samples of the many other unidentified bodies at overflowing local mortuaries and that dozens more cadavers would be ready for burial on Wednesday.

Aquino pledged aid to the slum communities hit by the disaster, which the government has said left 957 people dead and 49 others missing -- a toll they fear could rise as bodies swept out to sea begin to surface.

The president pledged to repair damaged roads and water systems, mass housing units in safe relocation areas, and water level sensors for all major river basins across the country to help communities avoid similar disasters.

He said he would sign an order declaring a national "State of Calamity" to make the necessary funds available.

"But in return we expect you to refrain from moving back to those places that put your lives at constant risk," Aquino said in a speech at an evacuation centre.

Unicef, the United Nations children's agency, appealed for $4.2 million (3.2 million euros) on Tuesday to help an estimated 200,000 children who are victims of the flood.

Meanwhile the UN Secretary General's Special Representative on Disaster Risk Reduction, Margareta Wahlstrom, said the Philippines should draw lessons from the natural disaster.

"The first is that more must be done to ensure early warning systems are effective in an age when climate change is intensifying the impact of typhoons," she said in a statement from the UN information office in Manila.

"The second is to understand the deadly cocktail of exposure and vulnerability created by poverty, rapid urbanisation and deforestation which results in huge loss of life, homes and hard-won development gains when a storm of this magnitude strikes."

Officials and experts said many of the dead were informal settlers living in shantytowns built on river sand bars made up of soft and unstable sediment.

But Cagayan de Oro Mayor Vicente Emano said that despite the president's words, he would be unable to stop survivors returning unless the government can offer them homes elsewhere.

"These people will insist on going back because they have no other place to go back to. Are you going to shoot them?" he said on ABS-CBN television.

Washi brought heavy rains that swelled rivers, unleashing flash floods and landslides that struck in the dead of night.

The death toll rose sharply Tuesday as the bodies of people who were swept out to sea were recovered.

"It (the death toll) is still going up and it will reach a thousand. There are still cadavers floating at sea," Benito Ramos, the civil defence office chief told AFP.

A British national was among those killed by the storm, Britain's Foreign Office said.

Authorities likened the impact to Ketsana, one of the country's most devastating storms which dumped huge amounts of rain on Manila and other parts of the country in 2009, killing 464 people.