Troops and special police forces have killed or arrested more than 100 rebels who occupied the coastal areas after government forces foiled what officials said was an attempt by the heavily armed insurgents to take control of city hall on Sept. 8.
Seven civilians have been killed in the fighting.
Troops have tried to contain the clashes on the outskirts of Zamboanga, a largely Christian city of nearly 1 million people, but suspected rebel mortar fire destroyed a car near the city's downtown area Monday, raising fears the gunmen were attempting to divert the military's attention.
Nearly 82,000 residents have fled the fighting into several emergency shelters, including the city's main sports complex.
Interior Secretary Mar Roxas said about 850 houses had been destroyed amid fierce exchanges of gunfire and occasional bursts of mortar rounds and grenades. Police said some fires may have been deliberately set by rebels to cover their escapes.
President Benigno Aquino III is in Zamboanga, a bustling port 860 kilometers (540 miles) south of Manila, to oversee the handling of the worst security crisis his administration has faced since he came to power in 2010.
The Moro insurgents, led by Nur Misuari, signed a peace deal in 1996, but the guerrillas did not lay down their arms and later accused the government of reneging on a promise to develop long-neglected Muslim regions in the south of the predominantly Roman Catholic nation.
The rebels have become increasingly restive in recent months as they've been overshadowed by a rival rebel group that engaged Aquino's government in peace talks brokered by Malaysia. The talks have steadily progressed toward a new and potentially larger autonomy deal for minority Muslims in the south.