More than 100 soldiers and supporters of jailed former Muslim separatist leader Nur Misuari have either been killed or wounded in some of the most intense fighting in the region in years.
"It's either surrender or nothing. They should lay down their arms and surrender to me those who killed my soldiers," said chief of the military Lieutenant-General Alberto Braganza on Thursday.
"Our operations will continue and we are trying to contain the fighting in some areas," he said, adding that reinforcements dispatched to the area were enough to crush the rebels.
Clashes erupted on Jolo on Monday following attacks by Misuari's men against troops in several towns.
Abu Sayyaf captured foreigners
and killed two in 2000 and 2001
The military said at least 20 soldiers have been killed and 38 wounded on its side. The rebels reportedly suffered more than 60 dead and wounded.
At least 500 families from five towns have been evacuated to safer areas in Jolo, a known stronghold of armed Muslim rebels and the al-Qaida-linked Abu Sayyaf.
Officials said the hostilities were set off after Misuari's men joined forces with the Abu Sayyaf, who were trying to repel a massive offensive by troops launched last week.
The Abu Sayyaf seized dozens of mostly European captives from a Malaysian resort and took them to Jolo in 2000.
The victims were later ransomed off one by one under the glare of the international media spotlight. In 2001, the Abu Sayyaf again captured several people, including three Americans, two of whom later were killed.
Misuari is the founder of the former separatist group Moro National Liberation Front (MNLF), which signed a peace pact with Manila in 1996.
He is in jail while on trial for a failed rebellion in 2001 that left more than 100 people dead in Jolo.
Officials said his followers demand that his detention be transferred to Jolo, many of whose local officials were at one time or another MNLF leaders.