More than half a million people in the southern Philippines have been affected by flooding after water lilies clogged the country's second longest river, officials said.

The lilies smothered a section of the 320 kilometre (200 mile) Rio Grande, preventing the water from emptying into the Moro Gulf to the southwest of Mindanao island after strong rains over the past week, authorities said.

The Rio Grande is the longest river in the Philippines' main southern island of Mindanao, and is the country's second biggest river system overall.

"Twenty-three municipalities are already flooded, affecting 559,067 people," regional social welfare head Pombaen Kader told AFP by telephone from the southern city of Cotabato.

Water levels started going up in recent days owing to heavy rain, and "the river flooded its banks because water could not pass through thick water lilies", she said.

Kader said the water had reached rooftops in some places, forcing authorities to evacuate more than 1,000 people. Many others had refused to leave, despite their homes being partially submerged, she said.

Troops have been struggling to cut through the packed water lilies while battling intermittent rains and strong currents, regional military spokesman Colonel Prudencio Asto told AFP.

"We had about 400 to 500 soldiers helping out in the effort. They are trying to cut through the growth using chain saws," Asto said.

He said that last week the water lilies covered up to 25 hectares (62 acres) of water.

"The growth was about 10 feet thick in some areas and so tightly packed that they (troops) could walk on top of it," Asto said.

"We are racing against time because forecasts of more rains could complicate the situation."