More than 200 millimetres of rain fell in the capital in the 24 hours to Wednesday morning, Escullar said, which was “not unusual”.
More heavy rain was expected on Thursday.
Landslides killed a pregnant woman and three children in Batangas province, south of Manila, and a woman and her five-year-old child in Pampanga province, north of the capital, police and disaster officials said Wednesday.
Three major roads were blocked by landslides in the mountainous Benguet province.
That takes the death toll from heavy rains over swaths of the country in the past two weeks to at least 14, as tens of thousands sheltered in evacuation centres.
President Ferdinand Marcos ordered on Wednesday disaster response officials to ensure they had sufficient stockpiles of food for the hardest-hit areas because “their situation is critical”.
Hard-scrabble neighbourhoods near Manila Bay were badly affected, with most of the streets underwater and more than 2,000 people forced to flee their homes.
About 20 big storms and typhoons hit the Philippines or its surrounding waters each year, damaging homes and infrastructure and killing dozens of people.