Heavy rain and floods have left 11 dead in the central and southern Philippine islands, including in a city still reeling from deadly guerrilla attacks, civil defence officials said Tuesday.

Among the hardest-hit areas was Zamboanga City, where floods again displaced thousands of people who had previously fled their homes to escape three weeks of fighting between Muslim rebels and government forces.

Three bodies were found in the southern city on Tuesday while troops plucked shivering children out of knee-deep floodwater, said the area's civil defence chief Adriano Fuego.

"This is the worst flooding to hit the city in recent years," he told reporters.

"Considering all we just went through with the (Muslim rebel) crisis, this is just so sad."

Hundreds of members of the Moro National Liberation Front battled troops and police in six Zamboanga districts from September 9, leaving 244 people dead, 116,000 people displaced and thousands of homes razed.

At the city's sports stadium, the rain has transformed a football field used by refugees from the fighting into a muddy lake.

People used garbage bins and chicken wire fences as makeshift platforms to raise their tents above the brownish water, eyewitnesses saw.

On the central island of Negros, the civil defence office reported six people drowned.

Two others, including a five-year-old girl, died in flash floods on the central island of Panay, the office said.

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