Fighting between armed followers of Nur Misuari, a jailed politician and former separatist leader, and security forces was concentrated in four towns in Jolo, a known guerrilla stronghold.
Thirteen Philippine soldiers were killed in a rebel ambush in the town of Patikul on Monday, Lieutenant-Colonel Buenaventura Pascual said on Tuesday.
Another soldier was slain in fighting in Panamao town on Monday.
The same day, two Muslim soldiers who were rebuilding a mosque as part of a civic project were killed in an attack in Parang, Brigadier-General Agustin Demaala said.
The military's southern command said 21 soldiers had been wounded in the clashes.
Demaala, commander of an anti-terrorist task force based in Jolo, said there were also reports of guerrilla casualties.
Scattered clashes were reported on Tuesday, and the military deployed at least two MG-520 helicopters to aid infantry men.
The separatist revolt started when at least 400 Misuari supporters attacked several Jolo military detachments at dawn on Monday, armed with rifles and other assault weapons.
Misuari supporters apparently thought they were being targeted as part of a massive military operation launched last week against leaders of the Abu Sayyaf.
The Abu Sayyaf captured tourists
and demanded ransoms in 2000
Military officials said they believed the Misuari faction had received help from the Abu Sayyaf, a Muslim group which the US and Philippine governments have linked to al-Qaida, based on Jolo island.
The Abu Sayyaf captured several European and US tourists several years ago, reportedly raising millions of dollars in ransom for some of the captives.
Two American captives were later killed.
Misuari supporters are now using the clashes to pressure the government into transferring their leader to a detention centre in Jolo, said southern command chief Lieutenant-General Alberto Braganza.
"They want him to be tried there," Braganza said.
Misuari was formerly the chief of the separatist Moro National Liberation Front (MNLF), which signed a peace treaty with Manila in 1995. He later became governor of a Muslim autonomous region until he was replaced in 2001.
He was arrested and jailed in a police camp near Manila after leading a failed revolt in Jolo to protest against his sacking in 2001.
Aside from the military outposts, security sources said Misuari supporters also targeted government projects including bridges, roads, and clinics.