Philippine President Benigno Aquino pledged aid Tuesday to communities hit by flash floods that walloped the south, as the official toll topped a thousand dead or missing.

Aquino flew to Mindanao island to inspect the ports of Cagayan de Oro and Iligan, choked with drying mud and crumpled homes, as well as hundreds of decomposing corpses that have raised health fears.

Mass burial plans for some of the dead that were announced a day earlier were called off Tuesday, with officials saying each would be fingerprinted and DNA samples taken from them first for future identification.

"I assure you the government will help you rebuild your homes. 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.

The government said 957 people are dead and 49 others are missing after flash floods ravaged the two port cities as well as nearby areas overnight Friday during the onslaught of tropical storm Washi.

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.

Aquino 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 in the future.

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

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

"They were underwater for the first three days but now, in their state of decomposition, they are bloated and floating to the surface," said Benito Ramos, the civil defence office chief.

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

A day after announcing mass burial plans for unclaimed bodies, the local governments of Iligan and nearby Cagayan de Oro said Tuesday that the justice ministry had insisted on proper documentation as well as individual tombs.

They said the burials will now have to wait until small teams of government forensics experts finish documenting each cadaver, a tedious process performed at overflowing mortuaries and, in the case of Cagayan de Oro, near a landfill.

"The mass burial is not just dumping them in a pit. We are building an apartment-type (mausoleum) with individual compartments. We can't just put them in all together," Cagayan de Oro city council member Alvin Bakal told AFP.

He said the city government was confident relatives would eventually be able to recognise and claim many of the 600-odd recovered bodies there so far, and the city was building tombs for just 40 unclaimed bodies.

Levy Villarin, health officer of Iligan, said the forensics team was taking an hour to document each body, and expects the process to take longer for about 300 bodies recovered there so far.

With dead bodies lying everywhere, there was controversy over Cagayan de Oro authorities' decision to bring 30 unclaimed cadavers close to a nearby landfill for temporary storage.

Pictures of the bodies, kept under a tent a few metres (yards) away from the dump where scavengers picked through piles of garbage for items to sell, caused outrage as they circulated on social networking sites.

"Looking for your mother, father, wife, husband, daughter, son, brother, sister who have been missing since Saturdays flash floods? Go to the citys dumpsite," Mindanews, a Mindanao-based news outfit, said on its website.

More than 284,000 people have been displaced by the storm with over 42,000 huddled in crowded, makeshift government evacuation centres.

Authorities likened the impact of tropical storm Washi 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.