Efforts to open schools in Manila for the first time since deadly floods descended into chaos on Monday, with some remaining under water and others occupied by homeless survivors with nowhere else to go.

The situation at schools in the worst-hit parts of the Philippine capital reflected wider problems in the government's response to the disaster, nine days after the heaviest rains in more than 40 years killed nearly 300 people.

As students were turned way from schools, mountains of debris were festering around Manila, more than 300,000 people remained in evacuation centres and one part of the city's outskirts was expected to be submerged into the new year.

"We were instructed to resume classes today but look around, the situation will likely not allow it," said Eliza Servesa, assistant principal at H. Bautista Elementary School in suburban Marikina.

Only three students in mismatched uniforms and carrying books salvaged from the floods arrived for morning classes, whereas before the disaster the school bustled with 3,500 children.

Marikina was one of the worst-affected by tropical storm Ketsana, which produced flood waters that rose six-metres (20-feet) high and washed away entire neighbourhoods along river banks, affecting nearly 3.9 million people.

In the immediate aftermath of the disaster, the government closed all schools in Manila for one week and allowed many of them to become makeshift evacuation centres for people whose homes were flooded or destroyed.

Late last week, almost 700,000 people were seeking refuge in such shelters, and the government said on Monday that 319,000 people were still staying in them with nowhere else to go.

At the H. Bautista elementary school, many of the nearly 5,000 people who initially stayed there had left -- either returning to their damaged homes or going to stay with relatives -- but between 300 and 500 remained.

"We can't force them to leave. That is against humanitarian principles," Servesa said.

Mother-of-two Ailyn Evangelista, 39, said leaving the school would eliminate all hope for her family.

"Here we have water, and toilets we can use. And if the flood waters come again we can run to the second floor. Also, we won't have to beg," she said, adding that relief items were being delivered regularly by various charities.

"Nobody wants to stay here if they still have a house to go to. But we don't."

Eduardo Tan, his wife and two children aged five and seven, had also bunkered in a hallway, creating a fenced-in space using desks.

"We want to leave of course, but where to go is the problem," said Tan, 48.

At the nearby Santa Elena High School, only about 20 percent of its 5,000 students showed up on Monday, and principal Elizalde Cena was forced to let them go at midday as teaching was impossible in the mud-filled classrooms.

"All our records were lost. I have yet to begin doing a proper accounting of my students," Cena said.

Officials in the worst affected areas of Manila said many of the schools in their districts were unable to open as scheduled on Monday, either because the rooms were still under water or occupied by evacuees.

Pateros mayor Joey Medina said that, with about half the district still under water, he had ordered its 10 public schools to resume classes on Wednesday instead.

"This is to give our school and local government officials sufficient time to clean up and ensure the safety of the returning students," Medina told reporters.