The victims died when a landslide buried their homes in thick mud, The Philippine Star reported Tuesday.
Chief Superintendent Mario de la Vega of the Quezon City Police District said the dead included a 23-year-old woman and her three children.
Several residents in flooded Caloocan City were trapped on the roofs of their homes, said Mayor Recom Echiverri.
In Bataan province, a child was reported missing after being swept away by a flash flood that hit his town.
Tuesday's torrential rains surpassed the amount of rainfall from Tropical Storm Ketsana that inundated a huge part of metro Manila and nearby areas in 2009, Inquirer.net reported.
Philippine President Benigno Aquino III told a press briefing infrastructure is needed to mitigate the effects of yearly floodwaters.
"It does not seem acceptable that every rainy season it's the same situation over and over again," Aquino said. "We need to put up structural interventions."