The Philippines army is sending extra troops to the southern island of Jolo after fierce fighting with rebels left more than 50 people dead.
Lieutenant-Colonel Buenaventura Pascual said the army had killed about 40 separatist rebels and lost 20 soldiers.
There is no independent confirmation of these figures.
The clashes began on Monday, when more than 500 rebels loyal to separatist leader Nur Misuari attacked troops in retaliation for a recent army assault.
A huge military operation was launched last week, to target the armed Muslim group Abu Sayyaf - an al-Qaeda linked organisation which is also alleged to have ties with the Misuari faction.
Military officials say Misuari's supporters are using the attack on Abu Sayyaf as a pretext to pressurise the authorities to have Misuari transferred from a prison near Manila to one in Jolo.
Misuari used to be the head of the separatist Moro National Liberation Front (MNLF), which signed a peace treaty with Manila in 1996.
But the violence continued and Misuari was jailed on charges of rebellion in 2001.
The latest skirmishes have been concentrated in several towns around Jolo, a known stronghold for Islamic militants.
Muslim rebels fired mortar shells at a military camp in Patikul town on Wednesday, but most of the fighting is thought to have taken place in the coastal town of Panamao.
Civilian residents of Panamao are being moved from the area, officials told the French news agency AFP.
Brigadier General Agustin Demaala said he was urging the rebels to stop their attacks, stressing that Abu Sayyaf - not followers of Nur Misuari - were the target of the recent government offensive.