Lyndon Barbers, the provincial governor of Surigao del Norte, said 66 people were rescued on Saturday afternoon while a passing boat rescued passengers and crewmen early on Sunday. Coast guard personnel rescued two crew members off Hinatuan island.
The bodies of seven passengers were taken to an emergency centre in Surigao city.
Coast guard officials said there was no major storm in the area, but that the ferry sank when it encountered rough seas and rain while travelling from Surigao city to Siargo Island, around 800km southeast of Manila.
A passenger list recorded only 48 names and authorities initially said 18 people were missing but the number grew as more people came forward to report their relatives had been on the ferry.
The boat had the capacity to carry 150 people.
Blance Gobenchiong, a regional director of the office of civil defence, said: "We have no idea how many people were actually on the boat."
He said that many travellers jump on board after inspection by the coast guard.
Those missing from the ferry include the mayor of Del Carmen, a town on Siargo Island, and a group of students who had attended a conference in Siargao city.