About a dozen leaders of the Abu Sayyaf, a group blamed for the country's worst terrorist attacks, have been killed or arrested in the past seven years after Manila allowed US Special Forces to deploy to the south.
Though barred from combat, the American troops have provided intelligence and training that helped local troops make headway in counter-terrorist operations, said chief of staff General Alexander Yano.
"We have not really confirmed an acknowledged leader," he told the foreign correspondents club here.
"Some leaders have emerged but we cannot confirm a single leader in the stature of [Abu Sayyaf founder Abdurajak] Janjalani who could have welded together the Abu Sayyaf Group into a united, formidable group," he added.
The group has been blamed for the kidnappings of western tourists and Christian missionaries as well as deadly bombings of ferries, shopping malls and buses.
Yano said Abu Sayyaf had become a "loose organisation" and its remaining members, whom he estimated to number 360, were scattered across the southern islands that are the heartland of a longstanding Muslim separatist insurgency.
"The leadership vacuum being experienced now is one of the reasons why they have to generate funds" through kidnappings, he said.
An abducted local television crew was freed in southern Jolo island earlier this month after at least PHP5 million (Dh412,875) in ransom was paid.
Yano said Filipino troops were conducting "precise surgical moves by specially trained forces that can strike when good intelligence comes in".
He described the role of the US forces in the southern Philippines as "more of a technical and training" role.
"They don't participate in any combat actions, but they assist us in terms of training our forces."
The help of the United States – which lists Abu Sayyaf as a foreign terrorist organisation and has paid bounties for the arrest or killing of its leaders – had been significant, Yano said.
"Most of the neutralisation of the high-value targets, the high-profile targets that we have neutralised in the recent past were effected with assistance from our counterparts. They are a big help."
He confirmed that the Americans also helped Filipino forces track the kidnappers of the ABS-CBN television crew during the nine-day hostage crisis in Jolo.
A suspect in the kidnapping, Jul Akram Hadjail, was detained on Wednesday at Jolo airport, a military spokesman said without elaborating.
An Australian think-tank warned on Wednesday that Southeast Asian terror groups still pose a "very real" and strategic threat requiring vigilance from regional governments, despite a drop in attacks.
"The strategic threat from terrorism remains multifaceted and real" especially in the region's "ungoverned spaces", such as Mindanao, where a religious conflict festers, said the report by the Australian Strategic Policy Institute.
Meanwhile, Abu Sayyaf abducted five workers of the Basilan Electric Co-operative on Basilan island on Thursday, the company said.