The Philippine government is deploying extra troops to the south after some of the bloodiest clashes with militants left more than 50 people dead.
The military said it had lost 26 soldiers and killed around 31 militants in three days of fighting on the volatile island of Jolo.
Thursday saw the heaviest toll after militants ambushed a military convoy.
The military said the arrival of extra forces would bring to 4,000 the number of troops stationed in the area.
Government troops, backed by US military trainers, have been fighting Islamist militants affiliated to various groups who have been hiding in the island's mountainous terrain for several months.
"As far as I can remember, this is our biggest casualty day"
The stakes were raised last month after 14 marines were killed on nearby Basilan island, with 10 of them beheaded.
Militants from Abu Sayyaf and the Moro Islamic Liberation Front (MILF) were suspected of being behind the attacks.
Gun battles
Abu Sayyaf and rogue elements from another group, the Moro National Liberation Front (MNLF), were blamed for Thursday's fighting near the town of Maimburg.
A troop convoy was ambushed on its way to the town early in the morning, leaving 10 soldiers dead.
Guide to Philippines conflict
Fifteen more soldiers were killed and 17 were wounded in gun battles that went on late into Thursday night after troop reinforcements were flown in to engage with more than 100 militants.
"As far as I can remember, this is our biggest casualty day," Lt Col Bartolome Bacarro said.
He said intelligence reports showed 27 militants had been killed and 25 wounded, although the militant groups had carried away most of their dead.
The skirmishes began in Jolo, some 950km (600 miles) south of the capital, Manila, on Tuesday.
Troops and militants clashed in Indanan town, wounding two marines. A day later a gun battle around Parang township killed one soldier and four militants.
The MNLF, which signed a peace deal with the government in 1996, claimed responsibility for Thursday's ambush, saying it was in retaliation for earlier army offensives.
But military officials have also blamed Abu Sayyaf, the group behind the Philippines' worst terror attack - a ferry bombing in 2004 that killed more than 100 people.
The US has listed Abu Sayyaf as a terrorist organisation and says it has links to Al-Qaeda, as well as the regional militant group Jemaah Islamiah.
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