Almost a million people have been forced to flee their homes in the Philippine capital of Manila after 11 days of constant rain put more than 60 per cent of the bustling metropolis underwater.

Sixteen people were reportedly killed on Wednesday, bringing the death toll to 64 since steady rains started when Typhoon Saola hit northern portions of the main Luzon island in late July.

Schools and many businesses remained shut for a second straight day, with the military, police and civic officials struggling to deliver aid as water swept through the city, turning major roads into rivers.

Rescue workers now face a race against the clock as waters continue to rise with thousands still marooned in their own homes.

Evacuation shelters in schools and basketball courts are bulging with families who are relying on government handouts to survive.

But with government resources already stretched, fears are growing of a full-scale humanitarian disaster.