The national disaster agency said 14,023 people, most of them from a flood-prone Manila suburb, had moved into evacuation centres.
Harsh weather has hit several parts of the world in recent weeks, bringing floods to China, India and Western Europe and heatwaves to North America, raising new fears about the impact of climate change.
The Philippines, a Southeast Asian archipelago of more than 7,600 islands, sees about 20 tropical storms a year but a warmer Pacific Ocean will make storms more powerful and bring heavier rain, meteorologists have said.
In some parts of the Philippine capital region, an urban sprawl of more than 13 million people, floodwaters, in places waist-deep, cut off roads to light vehicles.
The Philippines was already 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.
Roque said the public works ministry was busy clearing debris and landslides from roads in the provinces.
“Some houses were flooded up to the roof,” Humerlito Dolor, governor of Oriental Mindoro province south of the capital, told DZMM radio station.
Earlier on Saturday, residents of Metro Manila and nearby provinces were awoken following a 6.6-magnitude earthquake that struck the neighbouring province of Batangas.
The Philippine Institute of Volcanology and Seismology (Phivolcs) said the epicentre of the earthquake was southwest of Calatagan town in Batangas, the same province where an active volcano is threatening to erupt.
The earthquake, which struck at dawn on Saturday, was of tectonic, not volcanic, origin. A 5.1-magnitude aftershock was also reported.
Residents of the Philippine capital were already on alert on Friday, after the government raised some restrictions due to the increased number of COVID-19 cases due to the Delta variant.