Coast guard spokesman Lt. Cmdr. Algier Ricafrente says rescuers plucked 21 crew members from the water but two are missing.
He says officials are investigating how the 158-foot (48-meter) MV Bulk Carrier I and the larger Monrovian-registered MV HS Puccini hit each other Tuesday off Sarangani province.
Separately, officials are looking into reports of another cargo ship smashing into a fishing boat near Scarborough Shoal west of Luzon island.
The fishing boat's skipper Benito Otero says he and six crew members were rescued Wednesday after drifting for four days in their damaged craft, but two are missing.