Philippine authorities moved thousands of residents in the capital, Manila, out of low-lying communities on Saturday as heavy monsoon rains, compounded by a tropical storm, flooded the city and nearby provinces.

The national disaster agency said about 15,000 people, most of them from a flood-prone Manila suburb, had moved into evacuation centres.

"We decided to evacuate early," said Luzviminda Tayson, 61.

"We don't want the waters to rise and be caught," said Tayson, one of about 2,900 evacuees who were reminded to practice physical distancing as they took refuge in a primary school in Marikina city.

Harsh weather has hit nearly all corners of the globe in recent weeks, bringing floods to China, India and Western Europe and heat waves to North America, heightening fears about the impact of climate change.

The Philippines, a Southeast Asian archipelago of more than 7,600 islands, is hit by about 20 tropical storms a year but a warmer Pacific Ocean will make storms more powerful and bring heavier rain, meteorologists say.

In some parts of the Philippine capital region, an urban sprawl of more than 13 million people, flood waters waters rose waist-high in places and cut off roads to light vehicles.

The Philippines is also grappling with one of the worst outbreaks of COVID-19 in Asia and has tightened curbs to prevent the spread of the more infectious Delta variant.

With more than 1.54 million cases and 27,131 deaths, the Philippines has the second highest number of COVID-19 infections and fatalities in Southeast Asia, after Indonesia.

The public works ministry was busy on Saturday clearing debris and landslides from roads in the provinces, presidential spokesperson Harry Roque said in a statement.

"Some houses were flooded up to the roof," Humerlito Dolor, governor of Oriental Mindoro province south of the capital, told DZMM radio station.