The MV Josille 2 sank near before midnight Tuesday near an island off the resort town of El Nido in Palawan Island, said coast guard spokesman Lt. Cmdr. Armand Balilo.
One of the passengers managed to contact the coast guard, sparking a search that also involved the Philippine navy and local fishermen. Rescuers plucked the bodies of three women and two men at sea, officials said.
Navy Commodore Alexander Lopez said authorities were not sure how many people were on board the boat because the dead and rescued have already exceeded the manifest count of 46.
Navy, coast guard and fishing boats would continue a search in the rough waters, but strong winds prevented military planes from participating, Lopez said.
Many of the rescued passengers have returned to Liminangcong village in Palawan's Taytay town, where the Manila-bound boat originated, he said.
The onset of the typhoon season brought heavy rains, flash floods and strong waves in southern Mindanao region, where 75 fishermen and villagers were rescued while 13 others are still unaccounted for, regional military spokesman Maj. Jake Obligado said. He said search and rescue operations were ongoing.
Three days of flooding in several southern provinces displaced nearly 3,000 families and at least two drowned in Sarangani's Glan town, said Benito Ramos, head of the Philippines' disaster response agency. Those who fled were being sheltered in public gymnasiums and other government buildings.
A new storm in the western Pacific was forecast to reach the eastern Philippines later this week and could become the first typhoon of the year. About 20 tropical storms and typhoons each year batter the Philippine archipelago.