Lieutenant-Colonel Ernesto Torres, an army spokesman, said about 100 fighters from the Abu Sayyaf and a rogue faction of the MNLF were believed to be behind the ambush in the morning, retaliating for losses in an earlier clash.
The tropical isle of Jolo, in the largely Catholic country, has seen an escalation in violence after the army started collecting unlicensed guns from civilians.
On Wednesday, soldiers killed four Muslim fighters in a brief gun battle in nearby Parang town, where a soldier was also killed and five were wounded.
But the mainstream MNLF, which signed a peace deal with the government in 1996, claimed it was behind the ambush, saying it was retaliation for the deaths of five people during an army offensive a day earlier.
"It was not the Abu Sayyaf," Hatimil Hassan, the deputy chairman of the MNLF, said on local TV.
"It was our troops. It was the military's fault. They started it all."
Last month, members of the Moro Islamic Liberation Front (MILF), the country's largest Muslim separatist group, killed 14 soldiers in an attack on the nearby island of Basilan.
Many of the soldiers were beheaded but the MILF, which is meant to be talking peace with Manila, has denied its members mutilated the troops.
The military also blames members of the Abu Sayyaf for the decapitations.
Due to family ties on Jolo and Basilan, there are close links between the Abu Sayyaf, the MNLF and the MILF and sometimes an overlap in membership.
Elusive peace deal
The Philippine government wants to seal a peace deal with the MILF but has sworn to crush the Abu Sayyaf, which is blamed for the Philippines' worst terror attack - a ferry bombing that killed more than 100 people in 2004.
The islands of the southern Philippines, especially Jolo and Basilan, are hotbeds of extremism. They are also home to bandit and pirate gangs that prey on shipping in the South China Sea.
About 13,000 Philippine troops are on the islands with the stated objective of routing out about 2,000 fighters.
Around 100 US special forces are also on Jolo to help train the Philippine military, but they are forbidden from fighting under Philippine law.