The bodies of four children were found overnight, pushing the toll to 27.
The Maejan had set off from Calayan island for Aparri town in northern Luzon when it was hit by strong waves and capsized near the mouth of the Cagayan river on Sunday evening.
Gimotea said that the coastguard does not have a station at Calayan and could not prevent the overloaded vessel from sailing, adding that the vessel had all the correct permits.
A board of inquiry is investigating the incident but is mainly concerned with its cause and is not looking to file charges, he said.
The waters where the ferry capsized remained rough on Tuesday, hampering search and rescue operations, Gimotea added.
Sea accidents are common in the Philippine archipelago because of tropical storms, badly maintained ships and weak enforcement of safety regulations.
Last month, a cargo ship sank in rough seas north of Cagayan, and passing vessels plucked 16 of 20 people from shark-infested waters.
Weeks earlier, separate storms capsized two passenger boats in the central Philippines, drowning more than 50 people.