The daring assault sparked a brief clash that killed one attacker and a jail guard. The attackers and prisoners fled in several vehicles toward Basilan's jungle-covered mountainous heartland, Sakalahul said.
At least 31 inmates escaped, including five militants from the Moro Islamic Liberation Front, a large Muslim rebel group engaged in peace talks with the government, and 12 from the smaller but more violent Abu Sayyaf group, which has been linked to al-Qaida, regional military commander Maj. Gen. Benjamin Dolorfino said.
Among those who escaped was Dan Asnawi, a Moro rebel commander, and another guerrilla who have been accused of beheading 10 marines during a 2007 clash, regional marine spokesman Maj. Joel Lazo told The Associated Press.
"All these are high-risk prisoners," Sakalahul said, adding troops, backed by air force helicopters, were closing in on some of the fleeing inmates. None had been caught by late Sunday, however.
Military checkpoints were set up in Isabela, the provincial capital, and nearby townships, Dolorfino said.
The rundown provincial jail has had a history of jailbreaks. Three Abu Sayyaf militants, also accused of beheading the 10 marines, escaped in December last year after overpowering their guards. At least 16 people, including four Abu Sayyaf members, escaped in 2007.
In the biggest jailbreak, 53 of the prison's more than 130 inmates overpowered their guards using a smuggled pistol and fled in 2004. Nineteen Abu Sayyaf members were among those who escaped, police said.
Sunday's jail attack was the latest violence in the southern Mindanao region, scene of a decades-long Muslim separatist rebellion.
It occurred hours before Defense Secretary Norberto Gonzales and military chief of staff Gen. Victor Ibrado flew to Basilan, a predominantly Muslim island 550 miles (880 kilometers) south of Manila, to meet Roman Catholic church leaders who have appealed for martial law to be declared in the province amid recent kidnappings blamed on Islamic militants and the beheading of one hostage.
President Gloria Macapagal Arroyo imposed martial law in nearby Maguindanao province last week to allow troops to crack down on a powerful political clan blamed for the savage massacre of 57 people, including 30 journalists, on Nov. 23.
Arroyo lifted martial law in Maguindanao on Saturday but the province remains under a state of emergency.
More than 4,000 troops have been deployed there to restore order, disarm hundreds of militiamen loyal to the Ampatuan clan and arrest suspects in the massacre and a rebellion that the government alleged was waged by clan members. Thousands of assault weapons and large amounts of ammunition have been dug up in or near the clan's mansions and warehouses.
On Thursday, about 15 former pro-government militiamen who turned to banditry abducted more than 70 teachers, students and villagers in Mindanao's Agusan del Sur province after police tried to arrest them on murder charges.
They initially released several schoolchildren and women, then freed the remaining 47 hostages on Sunday after government officials pledged no arrests would be made.