Philippine troops are battling their way into coastal villages where Muslim rebels have held scores of residents hostage in a six-day standoff.
The move sparked fierce clashes that have killed 56 people and displaced more than 60,000, officials said on Saturday.
Interior Secretary Mar Roxas said government forces surrounding about 200 fighters from a Moro National Liberation Front rebel faction have started to advance and slowly retake rebel-held areas and clear roads in villages in the coastal outskirts of Zamboanga, a major port city.
Military spokesman Lieutenant Colonel Ramon Zagala said the offensive was "calibrated" to protect the unspecified number of hostages still held by the rebels.
Troops have not resorted to heavy artillery fire, rockets or launched airstrikes to protect the hostages and civilians.
Officials said that 47 of the 56 deaths were from the rebel ranks. The remaining nine deaths included four civilians, two soldiers and three policemen.
Aside from the hostages, the rebels have reportedly detonated bombs to set dozens of houses on fire to slow the troops' advance.
In rebel-held Santa Catalina village, the Associated Press reported that troops advanced behind armoured carriers to retake a road stretch only to be stalled by rebel fire, clusters of burning houses and apparent hostages yelling: "Don't fire, don't fire."
Several hostages have escaped but it remained unclear how many remained in rebel custody.
President Benigno Aquino III said more firefights were expected but assured more than 62,000 displaced villagers being sheltered at a sports complex in Zamboanga city that the rebels' capability to sow trouble has been degraded and the government was working to end the crisis soon.
Although the fighting has been contained in just three coastal villages by Saturday, Roxas said the danger to the trading city of nearly a million people remained serious and its international airport would have to remain closed, along with the main seaport.
The hostage standoff, the most serious security crisis Aquino has faced since rising to power in 2010, began on Monday when troops foiled an attempt by the rebels.
The rebels arrived by boat from outlying island strongholds, to march and hoist their flag at Zamboanga's city hall. They entered five coastal villages and took more than 100 hostages as human shields.
The Moro insurgents, led by rebel leader 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 government says Misuari kept on stalling and making new demands. He has not been seen in public since the standoff began.