Two people were killed by a collapsing wall as heavy rains pounded the Philippine capital Tuesday, bringing floods that have been worsened by garbage clogging the city's sewers and drains, officials said.

Waist-deep floods swamped low-lying areas of Manila after a dam near the city overspilled and had to open its gates, swelling rivers downstream, said Anna Orallo of the National Disaster Risk Reduction and Management Council.

The capital recorded its first deaths from the weather early Tuesday when two residents of a northern Manila suburb were crushed to death after a "stone wall beside their house collapsed because of the rain", Orallo told AFP.

Teams were deployed throughout the capital to provide help in case the flooding worsened, said Francis Tolentino, head of the Metro Manila Development Authority.

Tolentino blamed much of the flooding on waterways being clogged by garbage dumped into storm drains and sewers.

"The garbage is the main source of our floods. The whole nation needs to find a way to lessen the garbage," he said in an interview with ABS-CBN television.

At least seven domestic flights were cancelled due to the bad weather.

Authorities warned a brewing storm would continue to dump rains over the main island of Luzon, possibly bringing landslides and more flooding to the region.

The Philippines endures an average of 20 major storms a year, which often cause deadly flash floods and landslides.