Authorities rescued 40 people on Thursday after the vessel sank in strong winds, meaning it was carrying many more passengers than it was designed for, the coast guard said.
"We have called for investigation already, including on our personnel," coast guard spokesperson Armand Balilo told CNN Philippines television, adding that complaints would be filed against the boat's captain and operator.
The vessel was designed for roughly 40 passengers but it remains unclear how many people were allowed to board. The manifest showed only 22 names, the coast guard said.
Search and rescue, and retrieval operations are ongoing, Balilo said.
It is the second-deadliest in the Southeast Asian nation this year, after 33 people died in a ferry fire in the southern Philippines in March.
The country was this week hit by Typhoon Doksuri which brought winds of up to 175 kilometers an hour to its northern and most populated Luzon island, where the capital Manila is located.
The country has a patchy record for maritime safety, with vessels at times sailing while overcrowded and many ageing ships still in use.