The country's coastguard said it was "still trying to get a complete picture" of casualty numbers following the accident, which happened as the vessel sailed to the eastern island of Polillo in rough weather.
Army helicopters and coastguard boats were heading to the site, off the town of Real in Quezon province, but rescue operations were hampered by bad weather and huge waves caused by a typhoon.
"We heard about casualties, but we are still trying to get a complete picture," said coastguard spokesman Armand Balilo, the Independent reported.
Philippine media reported that at least three people had been killed.
Balilo said the ferry, which had the capacity to carry 280 people, had not been overloaded.
Boat accidents are common in the Philippines, which is frequently lashed by storms and typhoons.