At least 18 government soldiers and Abu Sayyaf militants were killed and 20 wounded as fighting between the two sides continued in Al-Barka town in Basilan, the military said on Wednesday.
The operation which took place from Sunday to Tuesday, was aimed at reducing the rebels' presence in the area.
Western Mindanao Command (Wesmincom) spokesperson Major Filemon Tan said they have already accounted three soldiers killed in the fighting, including a captain-rank commander, Xinhua reported.
Tan said the Abu Sayyaf has already suffered 15 deaths and seven wounded, though the military has not recovered a single body.
Tan said troops began advancing to the Abu Sayyaf lair last Sunday though the clashes became more intense last Tuesday when casualties began to pile up.
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"Up to now, sporadic fighting is ongoing. They (terrorists) are concealing themselves as troops continue to clear the area slowly. It (the clearing) is progressing slowly because there (Abu Sayyaf) are snipers," said Tan.
Tan also said that most of the soldiers who were killed and injured were hit by sniper fire. "If we become careless in our advance, we will have many fatalities," he said.
"We have yet to declare it clear because we have not reached the end portion of the camp," Tan said. He said the camp is located in a mountainous area and cannot be easily penetrated by armoured assets.