Philippine President Gloria Arroyo has temporarily moved the army headquarters to the south of the country, to boost operations against Islamist militants.
Twenty-five soldiers were killed in a single day of fighting
"I have ordered army commanding general Romeo Tolentino to the front lines," Mrs Arroyo said in a statement.
"The army headquarters will now be temporarily set up in Zamboanga until the situation normalises."
Fighting on Jolo island this week has left at least 50 people dead, 25 of them soldiers killed in a single day.
Following the clashes thousands of civilians have fled their homes on the island, which is some 950km (600 miles) south of the capital, Manila.
The new Defence Secretary, Gilbert Teodoro, Lt-Gen Romeo Tolentino and another top official, Gen Hermogenes Esperon, visited Jolo on Sunday, where an extra 1,000 soldiers have joined 4,000 already stationed there.
"The rule of law must prevail," Gen Tolentino told reporters.
The city of Zamboanga lies on Mindanao island, close to the flashpoint islands of Jolo and Basilan.
Jolo officials have appealed for food, water and medicines as people flocked to community centres and schools, fearing more fighting.
Troops backed by US military trainers have been fighting militants affiliated to various groups, hiding in the island's mountainous terrain.
Clashes broke out on Thursday when a troop convoy was ambushed near the town of Maimburg, leaving 10 soldiers dead.
Fifteen more soldiers were killed and 17 were wounded in gun battles after reinforcements were flown in to engage with militants.
The Moro National Liberation Front (MNLF) - which signed a peace deal with the government in 1996 - claimed responsibility for the 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.
Correspondents say the stakes were raised last month after 14 marines were killed on Basilan island, with 10 of them beheaded.