The escapees include five members of the Moro Islamic Liberation Front (MILF), the main separatist group negotiating an autonomy deal with the Philippine government for minority Muslims, Major General Benjamin Dolorfino, the regional military commander, said.
Another 12 are from the smaller but more violent Abu Sayyaf group, he added.
Major Joel Lazo, a marine spokesman, said the fugitives included Dan Asnawi, a Moro rebel commander, and another guerrilla accused of beheading 10 marines during a 2007 clash between troops and a combined force of Abu Sayyaf and Moro rebels on Basilan Island.
MILF 'not involved'
However an MILF spokesman on Monday denied any involvement in the jailbreak.
Eid Kabalu said only one escaped inmate was a Moro rebel while the rest were Abu Sayyaf fighters or common criminals.
The Abu Sayyaf group, linked to the Indonesian group Jemaah Islamiyah that aims to create a pan-Islamic state across Southeast Asia, has become infamous for a string of high-profile kidnappings.
It is also blamed for the worst attack in the Philippines – the bombing of a ferry in Manila Bay in 2004 in which 100 people were killed.
Cerge Remonde, a spokesman for Gloria Macapagal Arroyo, the Philippine president, said that the incident would not affect peace talks with the Moro rebels.
Talks resumed last week after a 16-month hiatus when the Philippine supreme court threw out a preliminary peace deal amid renewed clashes.
The jailbreak came on the same day tribal gunmen and government-armed former militiamen freed 47 villagers after four days of negotiations with authorities in the remote southern province of Agusan del Sur.
Under the agreement, the 15 gunmen were turned over to a Roman Catholic bishop while their murder cases, which they had wanted dropped because they stem from a clan feud, are reviewed by a tribal court.
The latest upheaval in the southern Philippines followed the November 23 massacre of 57 people, including 30 journalists and their staff, in Maguindanao province.
On Saturday Arroyo ordered the suspension of martial law imposed in Maguindanao following the massacre, but left more than 4,000 army troops to restore order and disarm paramilitary groups.