The ferry was travelling from the capital Manila to Mindoro Island in the southwest.
Commander Armando Balilo, a coastguard spokesman told Al Jazeera the rescued passengers were undergoing medical check-ups and believed to be in good health.
"There were fishermen in the area this morning and the probability that some of the passengers were taken by the fishermen is very big."
Balilo said the ferry was carrying 73 people, but it is not known how many were in the fishing boat. The cause of the collision is unknown.
Weather conditions were food in the area at the time of the collision.
Ferries form the backbone of mass transport in the archipelago nation of 92 million people, and sea accidents are common due to tropical storms, badly maintained boats and weak enforcement of safety regulations.
Last year, a ferry overturned after sailing toward a powerful typhoon in the country's central region, killing more than 800 people on board.
The world's deadliest peacetime maritime disaster occurred south of Manila in 1987 when the Dona Paz ferry capsized after colliding with a small oil tanker, killing more than 4,000 people.