Survivors of devastating Philippines flash floods face a growing threat of disease including cholera and typhoid, officials warned Wednesday as the death toll rose above a thousand.

Some 44,000 people who fled as huge torrents swept away shanty towns in the nation's south are packed in evacuation camps without proper sanitation, and officials fear the sites are potential breeding grounds for epidemics.

Tropical storm Washi struck the southern island of Mindanao over the weekend, bringing heavy rains, flash floods and overflowing rivers that swept whole coastal villages away.

Civil defence chief Benito Ramos put the death toll at 1,010 and warned it could climb further as victims swept out to sea began washing ashore, with some corpses turning up nearly a hundred kilometres (62 miles) away.

"They are washing up on the beaches," he told AFP. "I expect that (the toll) will go up because there are still many missing," he said.

Ramos said he expects the toll to reach around 1,100 but warned that many of the deceased who were swept to sea would never be found.

"In our experience, after three days, (a body) will emerge but after another three to five days, it will submerge again," he told AFP.

His office put the number of missing at 46.

Eighteen unclaimed corpses were buried in individual tombs in Iligan on Wednesday, after 38 were interred a day earlier, city official Teresita Herrera told AFP.

Officials said Wednesday that hundreds of decaying bodies and their overpowering stench had to be dealt with but attention should now focus on protecting the living, particularly in the shelters.

Assistant Health Secretary Eric Tayag warned the crowded conditions could lead to outbreaks of leptospirosis, diarrhoea, cholera, hepatitis A, typhoid fever, and dysentery, with children and pregnant women the most vulnerable.

Health Undersecretary Ted Herbosa said the government was bracing for possible outbreaks next week.

"There were no reported cases of illnesses yet but we are in constant monitoring of incident of diarrhoea and respiratory illness which we expect to emerge next week," he told reporters.

The areas hardest-hit by the storm were the port cities of Cagayan de Oro and Iligan, where crowded slums built on sandbars near the mouths of major rivers were washed away in the dead of night.

Conditions remain chaotic at the evacuation centres, mainly schools and gymnasiums, and with no running water fire trucks were being used to deliver supplies.

"The problem is we only have one or two toilets per school, and they have to cater to 3,000 or 4,000 users," Iligan health officer Levy Villarin told AFP.

Dante Pajo, a member of the Cagayan de Oro city council, said there was not enough food or water for the city's 26,000-plus evacuees.

At a Cagayan de Oro gymnasium, 52-year-old grandmother Adela Campaner lined up at mid-morning for bowls of porridge -- the first meal of the day for herself and her two grandchildren.

"I am ashamed that I have to beg for food," she said, vowing to return to their devastated riverside shanty town as soon as possible and resume her roadside restaurant business.

Wearing donated, mismatched T-shirt and pants, she said she had not taken a bath for three days and was forced to retreat from the school's toilet earlier in the day due to the repulsive smell.

The gym was packed beyond capacity with people sleeping on mats and sheets of cardboard that filled every available space.

Some 276,000 people are receiving emergency assistance, including many who have shunned the evacuation centres and are sheltering with relatives -- unable to return home as the government has forbidden them from returning to flood-prone areas.

"They have no houses, nothing to go home to. The clothes on their backs are all they have," Ramos said.