Thousands of people in the southern Philippines are facing Christmas in emergency shelters after floods that left more than 1,000 people dead and another 1,000 unaccounted for.

As government workers recovered more bodies of those killed when tropical storm Washi hit last weekend, one local mayor bleakly told those left homeless or bereaved by the floods that there would be "no Christmas" this year.

Tens of thousands of people are jammed in crowded evacuation centres, short of water and sanitation facilities.

"There is no Christmas," Vicente Emano, mayor of the hard-hit city of Cagayan de Oro, curtly said Saturday when asked if he would be delivering his traditional holiday message.

Washi spawned heavy rains, overflowing rivers and flash floods that wiped out whole villages, many built on riverbanks and sandbars in the coastal port cities of Cagayan de Oro and Iligan, which were the worst hit last Saturday.

The government civil defence agency put the toll of dead at 1,100 with 1,079 reported missing although it remained unclear if some of the missing were among the hundreds of unidentified corpses already recovered.

The storm and floods have displaced around 330,000 people with more than 69,000 others huddled in emergency shelters.

Just hours after the latest death toll was announced, village chairman Cairunding Embader said his staff had found 16 more dead bodies on the outskirts of Iligan City.

Emano said city employees and search team members would be working through the Christmas holidays, recovering bodies and caring for those who were evacuated from their homes.

To deal with the hundreds of dead, with the stench of decomposing bodies in parts of the city overwhelming, Emano said two large communal graves had been dug and unclaimed bodies would soon be buried in them.

While Christmas is normally one of the most festive times of the year in the Philippines, a largely-Roman Catholic country, few in the affected areas felt like celebrating.

"Because of this flood, I don't know if our Christmases will ever be merry," said Junie Legaspi, 32, a vendor who lost his house and livestock animals in the flood.

Huddled in an evacuation centre, wearing an ill-fitting woman's blouse donated to him, Legaspi fought back tears as he said his eight children would forever associate Christmas with the floods.

"This is the worst Christmas gift one can receive."

Regional social welfare director Araceli Solamillo said her agency was bringing in professionals to counsel depressed people at the centres.

"We have provided psychosocial intervention like stress debriefing with social workers. But we need more psychologists and trained social workers, we need volunteers," she told AFP.

Her department is also providing each family with a "Christmas meal" package so they can enjoy traditional holiday fare including spaghetti, fruit salad and canned meat to replace the usual Christmas ham.

International institutions, local charities and the government have been pouring in aid to alleviate the lack of water, toilets and space in the evacuation centres, mostly converted schools and gymnasiums.

Laundry worker Floresa Avenido, 31, said the flood destroyed her entire two-storey house, leaving her homeless but all of her four children survived.

"Even if we lost everything to the flood, I am still thankful because nobody is missing in our family. My family is the most important Christmas gift for me."