Among the casualties, two men drowned and a child was killed in a landslide in Camarines province. Three people died when a warehouse collapsed in Cavite province.
The casualty count is subject to validation by local officials and the disaster agency, which has so far recorded 14 deaths and three missing.
Tens of thousands of homes were submerged, although water levels started to recede in parts of the badly hit Marikina suburb, allowing residents to start cleanups after returning to homes covered in debris and caked in mud.
"We don't know how to start cleaning. Mud is so thick up to the second floor," Gilbert Gaston, a Marikina resident, told DZMM radio.
Many residents took refuge on rooftops and were among some 6,000 people rescued across Manila's suburbs. Government agencies were clearing landslides and debris elsewhere, Defense Secretary Delfin Lorenzana said.
About 500,000 households in and around the capital were without power and virtual classes and government work was suspended in Luzon, home to half of the Philippines' 108 million population.
Vamco was approaching central Vietnam, where devastating floods and mudslides since early October have killed at least 160 people. It is expected to make landfall on Saturday.