Thirty-four of the inmates had been recaptured by Thursday morning, adding to five who were killed on Wednesday
Suspected Muslim guerrillas stormed a decrepit jail in one of the major southern cities on Wednesday, freeing 158 inmates and killing a guard, in what authorities said was a bid to free fellow rebels.
Thirty-four of the inmates had been recaptured by Thursday morning, adding to five who were killed on Wednesday, jail authorities said, but they emphasised there were many obstacles in the manhunt.
"This is a very wide area. Aside from sugar, rubber and coconut plantations, there are areas and camps held by rebels that we cannot easily enter," jail warden Peter Bongngat told AFP.
The southern Philippines is home to a decades-old Muslim separatist insurgency, as well as extremist gangs that have recently declared allegiance to the Islamic State.
The southern region of Mindanao is the ancestral homeland of the Muslim minority in the largely Catholic Philippines.
The badly overcrowded jail in Kidapawan, 950 kilometres (590 miles) south of Manila, contained rebels from the various groups as well as members of criminal gangs that thrive in the corruption and poverty of the south.
The jail, which housed about 1,500 inmates, is a run-down former school building that militants have targeted repeatedly over the past 15 years.
In 2007, Khair Mundos, a Filipino who would later become one of the world's most wanted accused terrorists escaped along with 48 other inmates. Mundos, with a $500,000 bounty from the US government, was recaptured in Manila seven years later.
However Wednesday's jailbreak was the biggest in the nation's history, Bureau of Jail Management and Penology spokesman Xavier Solda told AFP.
Solda said 13 "high-value targets" -- seven Muslim rebels and six organised crime gang members -- had not been able to escape on Wednesday.
However Solda and Bongngat were not able to tell AFP who was still on the run, saying their identities were still being "verified".
On Wednesday, Bongngat said the attackers were believed to be militants who had broken away from the Moro Islamic Liberation Front (MILF), the nation's largest Muslim rebel organisation which is in peace talks with the government.
The MILF, which has about 10,000 armed followers, has been fighting since the 1970s for independence or autonomy.
The rebellion has claimed more than 120,000 lives although the MILF has in recent years observed a ceasefire as part of the peace process.
MILF spokesman Von al-Haq insisted Thursday that none of its members was involved in the raid, adding the group was willing to coordinate with government to allow searches in its communities.
"The commander named to be the leader of the raid was 100 percent a notorious criminal. He was never a member of the MILF," Al-Haq told AFP.
Al-Haq said the commander, known by an alias of Commander Derby, had broken into the jail to release a relative who was the leader of the Muslim inmates.
Al-Haq said the relative and the leader of the Christian inmates were among the first to escape, and remained on the run.