Heavy rains flooded evacuation centres in the southern Philippines, adding more misery for thousands of people displaced by a bloody Muslim rebel siege, officials said Saturday.

Almost a month after followers of Moro National Liberation Front (MNLF) leader Nur Misuari besieged Zamboanga, over 116,000 people -- around one tenth of the port city's population -- are still sheltering in evacuation centres, where there is a shortage of toilets and medicine.

But government tents have been unable to withstand the heavy rain which has been falling since Friday, causing knee-deep floods said Adriano Fuego, the area's civil defence chief.

"The waters are as high as knee deep in some places. It is mostly muddy (there) and the people are getting soaked," Fuego said.

Of the 71,000 people sheltering at the main evacuation centre in the city's sports stadium, 46,000 have had to be moved from their tents to higher ground, while the rest sheltered in the elevated stands, Fuego said.

The government has begun constructing raised plywood shelters with tin roofs to replace the tents with fears that thousands will not be able to return home for months, he added.

"No evacuation centres have closed because they still cannot return to their neighbourhoods since the clearing operations are still going on," he said, referring to police and military searches in the siege area for unexploded ordnance, booby traps, dead MNLF fighters and possible rebel stragglers.

The government declared the rebel action crushed on September 28 with the release of the last of 195 hostages, but the areas where the fighting took place are still largely off-limits to civilians until they are cleared.

However the heavy rains have also affected clearing operations, said police spokesman Chief Inspector Ariel Huesca.

"It is flooding in a lot of places, even at our offices at the police camp," he said.

Zamboanga police on Friday brought in another MNLF straggler found in a ruined house.

Hajar Hajun, said "I have been hiding in the ceiling, surviving by drinking rain water. I was afraid to surrender for fear I would be killed."

He was among hundreds of heavily armed MNLF fighters who entered Zamboanga City on September 9 in an effort to disrupt government peace talks with a rival Muslim group.

They took residents hostage and set fire to about 10,000 houses during three weeks of fighting with soldiers and police.

The military said an estimated 206 MNLF fighters, 25 government troops and 13 civilians were killed in the violence.

Police are continuing their search for Misuari following a raid on his Zamboanga City home on Friday which recovered explosives and documents but failed to catch the MNLF leader, Huesca said.

Muslim rebels have been fighting since the 1970s for an independent or autonomous homeland in the south of the mainly Catholic Philippines. An estimated 150,000 people have died in the conflict.