The death toll from a typhoon that devastated the southern Philippines earlier this month has topped 1,000 as hundreds more remain missing, the government said on Sunday.

Typhoon Bopha killed 1,020 people, mostly on the southern island of Mindanao where floods and landslides caused major damage on December 4, civil defence chief Benito Ramos said.

A total of 844 people remain missing, about half of them fishermen who ventured out to sea before Bopha hit, Ramos said, adding he feared many of the missing were dead.

"The death toll will go higher. We found a lot of bodies yesterday, buried under fallen logs and debris," he told AFP.

He added the toll from Bopha, the worst natural disaster to hit the country this year, would exceed the 1,268 confirmed dead after Typhoon Washi struck the southern Philippines in December 2011.

"We prepared. We were just simply overwhelmed," said Ramos.

"They did not expect this intensity. The last time (this part of the country) got hit by a strong storm was 1912," he added.

He added that many evacuation centres were destroyed by the typhoon.

More than 27,000 people remain in such centres almost two weeks after Bopha hit as the search for the dead and missing continues, the civil defence office said.

Colonel Lyndon Paniza, spokesman of the military forces in the worst-affected region, was less optimistic of finding any survivors.

"We are on (body) retrieval mode already. We are done with search and rescue," he told AFP.

Paniza, who oversees the hardest-hit regions which suffered over 960 dead, said he expected the death toll to rise further.

"It has been 12 days already so it looks like (survival chances) are doubtful," he said.

Among the casualties were seven soldiers who were killed and four who remain missing after they were hit by flash floods while doing relief work, he said.

In the southern town of New Bataan, which suffered over 500 dead, including 235 bodies that are still unidentified, people still struggled to recover, building makeshift shelters out of scrap wood and rags.

Town Mayor Lorenzo Balbin said the toll of the dead may even be larger than the official lists because many transients, who pass through the town of work on small-scale mines and plantations, do not even register as residents.

With no one to report them missing, their deaths may go unnoticed, he said.

The situation in the town, which was largely flattened by the typhoon, had improved slightly as more relief aid was reaching the area.

Trucks from government and private relief agencies were seen entering New Bataan, handing out much-needed food to villagers still stunned by the storm's fury.

Balbin said the focus now was on finding new crops to replace those destroyed by the typhoon.

The storm has caused massive damage to infrastructure and agriculture, destroying large tracts of coconut and banana trees.

The National Disaster Risk Reduction and Management Council initially estimated damage to crops and public infrastructure at 7.16 billion pesos ($174 million).

The Philippines is hit by about 20 major storms or typhoons each year that occur mainly during the rainy season between June and October. Bopha was the strongest typhoon to strike this year.