Soldiers had earlier discovered the headless bodies of six men close to Parang town.
Rafael said the beheadings may have been in response to the deaths of more than 70 Abu Sayyaf members, including two leaders, in an eight-month military offensive backed by US troops and equipment.
"This is a retaliation for the killing of one of their commanders," he said.
He said the company which employed the road workers had refused to pay a ransom.
The Abu Sayyaf, which is on a US list of terrorist groups, has been the target of a massive US-backed military offensive on Jolo that started in August and has killed its top two leaders.
The group gained international notoriety about five years ago when they captured and beheaded tourists and church workers, and its members still kidnap people for ransom to raise funds.
Loong has said that the kidnappings showed the Abu Sayyaf remains capable of banditry and terrorist acts despite a number of battlefield losses.
He said it was unclear whether the kidnappings were intended to divert troops who are hunting for rebel commander Habier Malik and his men from the Muslim Moro National Liberation Front.
Malik was blamed for deadly mortar attacks in Jolo last week.
An estimated 300 to 400 Abu Sayyaf fighters remain at large on Jolo, about 950km south of Manila.
The US has offered large rewards for the capture of Abu Sayyaf commanders.