A battalion of infantry, comprising about 500 soldiers, arrived on Sunday at the port of Jolo to bolster other army units as recent clashes left five soldiers wounded.
The military said its forces had surrounded about 100 fighters loyal to jailed Muslim politician Nur Misuari after six days of clashes that left more than 60 people dead.
Officials said the fighting also displaced up to 13,000 civilians in several towns on the island of about 400,000 people.
Fighting was reported around the town of Panamao on Saturday, leaving five soldiers wounded, said Brigadier General Agustin Dema-ala, commander of a joint anti-terrorism task force.
"We have a minimal number of casualties as we expand control of the area," he said.
"We are still encountering resistance, but the situation is manageable."
Dema-ala estimated that there were less than 100 armed Misuari supporters in a forested area near Panamao.
"Some have fled after they ran out of food and ammunition and after they failed to get reinforcements" from the local populace, he added.
"I don't think they are still capable of launching attacks, they have run out of ammunition already and they have lost support from the populace," said Lieutenant General Alberto Braganza, commander of military forces in the southern Philippines.
He said his men would "continue the pursuit operation to make those attackers and ambushers pay for their crime[s]".