Twenty-four Al-Qaeda-linked rebels and eight soldiers were killed as the military over-ran one of the extremists' main strongholds in the south of the country, officers said on Monday.
Troops on Sunday took control of the Abu Sayyaf group's biggest camp on the island of Jolo following rounds of air strikes, said Major General Benjamin Dolorfino, head of military forces in the south.
The military recovered the bodies of two Abu Sayyaf fighters, according to Dolorfino. "But based on intelligence reports we believe there are 17 more deaths on the Abu Sayyaf side," he told reporters.
However on Monday, as Philippine Marines were leaving the newly-captured camp, they were ambushed by Abu Sayyaf fighters resulting in the deaths of eight troopers and five guerrillas, said military spokesman Lieutenant Colonel Romeo Brawner.
Fourteen soldiers were wounded in two days of fighting including two forward air controllers who were with ground troops to direct the bomb attacks against the militants, the officers said.
Fighting had raged on Sunday between the military and as many as 200 Abu Sayyaf guerrillas, but the troops finally raised the Philippine flag over the mountainous area, said Dolorfino.
"This is very significant because this is their main sanctuary. This is the main stronghold of the Abu Sayyaf (on Jolo)," he said.
"We will build a detachment here so that their world will get even smaller."
However he cautioned that fighting was expected to continue as soldiers pursued the fleeing Abu Sayyaf members.
Abu Sayyaf reinforcements even came in by boat from the nearby islands of Basilan to help their comrades on Jolo, said regional military spokesman Major Ramon David Hontiveros.
The Abu Sayyaf was established in the early 1990s, allegedly with seed money from Osama bin Laden's Al-Qaeda network, to fight for a Muslim state in the south of this Catholic nation.
It has kidnapped dozens of foreign aid workers, missionaries and tourists in the south and was blamed for the country's worst terrorist strike, the bombing of a ferry in 2004 that killed over 100 people.
In another grisly incident, the Abu Sayyaf abducted three Americans off the western island of Palawan in 2001. One of the hostages was later beheaded while another was killed in the military's rescue attempt.
American troops have been in the southern Philippines since 2003 to train Philippine soldiers in how to combat the Abu Sayyaf.