Major-General Ruben Rafael said the bodies of the eight civilians were found away from the site of the operation in Maimbung, suggesting that they were killed in another incident.
"It was a legitimate operation and we're trying to find out how those civilians got killed," he said.
Two commandos and three Abu Sayyaf fighters were killed in a military operation in the area at the same time.
Major Eugene Batara, regional military spokesman, said that they were also looking into reports that the killings were part of a separate family feud.
|"It was a legitimate operation and we're trying to find out how those civilians got killed" |
Major-General Ruben Rafael, military commander
"There was fighting between two warring families in the area and the encounter and exchange of fire could have triggered the volatile situation between the families," he said.
Al Jazeera's Marga Ortigas, who witnessed the aftermath of the incident, said that many on the island believed that the military had been misled on purpose by their local guides.
She said that villagers had identified the guides as people involved in a dispute with the victims of the shooting.
Ortigas added that she saw three houses that had been burned down at the scene of the incident and that some villagers alleged that their homes had been ransacked.
But local officials said that residents claimed to have witnessed the commandos opening fire on civilians after being shot at as they arrived to carry out the operation.
Tan said he was informed by a village chief and some residents that one of those killed on Monday was a soldier on vacation.
"He was tied up and shot in front of his wife. Some of the civilians were shot in the head. These people were not caught in the crossfire, they were the targets."
Jolo, a majority Muslim island about 950km south of the capital Manila, was once portrayed as a success story in the Philippine military's battle to flush out the Abu Sayyaf but the group resumed kidnapping and decapitations last year.
The military's relations with the locals have deteriorated due to operations that have forced villagers from their homes.