Sakalahul accused fighters from the Moro Islamic Liberation Front (Milf) of being behind the attack, because at least two suspected members of the group were among those who escaped in the raid.
The two are accused of killing 14 Filipino soldiers in an attack in 2007.
Sakalahul said the attackers and prisoners later fled in several vehicles towards Basilan's jungle-covered heartland.
The Milf has long sought autonomy for the southern island of Mindanao island, but is currently in peace talks with the government.
If Milf's involvement is proved, Sunday's incident could mark a violation of a ceasefire between the group and the government.
Officials said another 29 inmates took advantage of the breach in the wall to also escape the prison, including members of the outlawed Abu Sayyaf armed group, officials said.
The Abu Sayyaf group has been linked to Jemaah Islamiyah, an Indonesian group that aims to create a pan-Islamic state across Southeast Asia.
It has become infamous for a string of high-profile kidnappings and is blamed for the worst attack in the Philippines - the bombing of a ferry in Manila Bay in 2004 in which 100 people were killed.