Members of the Bangsamoro Islamic Freedom Fighters (BIFF) attacked pro-government volunteers in the town of Midsayap before dawn but retreated when military reinforcements arrived, regional army spokesman Colonel Dickson Hermoso said.
One soldier was killed while residents reported seeing four dead BIFF guerillas being carried away by their comrades, the colonel added.
The rebels then took 15 schoolteachers and farmers to use as human shields against pursuit although they released some of them later, Hermoso said.
Three hostages remain and a local Muslim preacher has been sent to negotiate for their release, he added.
Both Hermoso and BIFF spokesman Abu Misry Mama said the latest fighting was not related to the three-week long conflict with another Muslim band in Zamboanga City, about 273 kilometres (170 miles) from Midsayap.
"This has nothing to do with the Zamboanga incident. That is different. Our enemies are the military. We want them out," Mama told radio station DXMS.
About 200 members of the Moro National Liberation Front (MNLF) entered Zamboanga, a major trading centre with one million residents, on September 9 in the most serious armed challenge to the Philippine government in recent years.
Despite the deaths of 102 rebels and the capture or surrender of over a hundred others, almost 50 MNLF fighters still remain, holding 20 hostages, said police regional spokesman Chief Inspector Ariel Huesca.
Fifteen soldiers and police were killed in the fighting which has seen the rebels burn hundreds of houses.
"Troops are cautiously moving in because of rebel snipers," said Huesca, adding he could not say when the crisis might end.
Both the MNLF faction of rebel chief Nur Misuari and the BIFF oppose ongoing government peace talks with the largest Muslim rebel group, the 12,000-strong Moro Islamic Liberation Front (MILF).
Muslim rebels have been fighting since the 1970s for an independent or autonomous homeland in the south of the mainly Catholic Philippines. An estimated 150,000 people have died in the conflict.
Misuari fears his MNLF would be sidelined by an impending deal with the MILF while the BIFF broke away from the MILF and continues to demand independence.