The storm, packing gusts of 90 kilometers (56 miles) per hour, moved out into the South China Sea before dawn after cutting through the central islands, the government weather station reported.
Rough waves capsized a small ferry off the southern tip of the main island of Luzon and two people on the boat are still missing, the Coast Guard said.
The eye of the storm passed near Bulusan volcano over the weekend, and "muddy stream flows" in waterways caused flooding of some roads near Irosin, a town near Bulusan, the Philippine Institute of Volcanology and Seismology (Phivolcs) said.
The 1,565-meter (5,134-foot) Bulusan has been spewing out ash in recent weeks although the institute says it does not believe that an eruption is looming. — AFP, Shiela Crisostomo