The motorboats — Che-che, Keziah and Jennyville — sunk near the port of Iloilo City on Saturday after capsizing because of strong monsoon winds.
According to Donna Magno, the City Disaster Risk Reduction and Management Office head, the Che-che boat was headed from Iloilo City to the island of Guimaras, while Keziah went in the opposite direction.
As of 02:30 GMT, out of passengers on board three capsized boats, 62 were rescued, 31 were confirmed dead, and 3 are still missing, Coast guard spokesman Armand Balilo said.
Search and rescue operations are underway, according to the authorities.
Southeast Asia has been under severe pressure as the monsoon season unleashed heavy rains, floods, landslides and other devastating disasters across the region. Hundreds of people have been killed, thousands more were injured or subjected to an emergency evacuation.