Troops overran a monitoring post used to help protect Fathur Rahman al-Ghazi in the south of the country, the military said on Tuesday.
Communications equipment and solar panels were seized from the hut in the town of Tungawan, but no arrests were made as the fugitives left hours before soldiers arrived on Monday.
"While government troops were closing in on their target, said armed group scampered from a makeshift hut leaving behind their communications equipment," the military's southern command said.
The men who fled are believed to be Filipinos protecting al-Ghazi, who has been on the run after escaping from a jail in the police headquarters in Manila last July.
Al-Ghazi is a self-confessed member of the Jamaa Islamiyah, which western intelligence agencies have accused of being linked to al-Qaida and blamed for a spate of bombings in Indonesia, including the Bali attacks that left over 200 dead last year.
At the time of his escape, al-Ghazi was serving a 17-year jail term for illegal possession of explosives. He has also admitted to helping plot a bombing campaign in Manila in December 2000 that left over 20 dead.
Meanwhile, the Philippines government and Muslim separatists in the south of the country still have not set a date to resume formal peace talks, according to officials on Tuesday.
Hereditary issues, in particular, seem to have prevented any kind of agreement on resumption of talks. Moro Islamic Liberation Front (MILF) spokesman, Eid Kabalu, said the issue “could be a stumbling block".
Kabalu highlighted the still unresolved issue of "ancestral domain" in the agenda, which he said "goes beyond the issue of land itself" and would cover "areas where they [Muslims] exercise their own socio-economic [practices] and culture."
MILF leader Hashim Salamat's
death postponed peace talks
Some MILF members are insisting the ancestral domain issue be settled first before the talks restart.
The Front has not yet delineated the areas it wants listed as ancestral domain, but the government is worried the areas might cover lands already in private hands or recently occupied by Christian immigrants.
Kabalu has already said the MILF panel was likely to "confine it (ancestral domains) to the areas where the Muslims are predominantly located."
Special government intermediary Norberto Gonzales said on Monday that the negotiations could resume in October.
To avoid clashes that might block the talks, "the government is proposing that a procedural mechanism should be put in place to identify what are these ancestral domains," rather than making them an issue in the negotiations, the source said.
This includes the completion of the "terms of reference" that would allow Islamic countries like Malaysia to dispatch "third party observers" who would monitor the ceasefire between the government and the rebel forces, Kabalu said.
Malaysia, which is hosting the planned talks between the Philippines and the MILF, has been asked to provide the bulk of third-party monitors, with Bangladesh, Bahrain, Brunei and Libya among others also asked to pitch in.
MILF has waged a 25-year struggle for a separate state in the southern third of the Philippines which, although once predominantly Muslim, has become majority-Christian following a post-independence policy of resettlement by Manila. Tens of thousands of people have died in the civil war since the 1970s.
A ceasefire is in place between the government and the MILF although sporadic clashes still occur.