Thousands more residents have fled, while sporadic clashes continued as soldiers moved to clear suspected Moro National Liberation Front (MNLF) fighters from coastal neighbourhoods on Sunday after a ceasefire plan collapsed.
Day and night operations by at least 3,000 elite government troops have now seen 51 fighters killed, with another 48 captured or apprehended, according to official government figures.
On the government side, at least six soldiers have been killed with another 79 wounded. Civilian casualties stand at four, with another 24 wounded.
The government figures also suggest 51 hostages have so far been released or have escaped.
“We are continuing to press forward with our calibrated military response,” Lieutenant-Colonel Ramon Zagala, military spokesman, told AFP news agency on Sunday.
“Fighting is continuing as we speak. They continue to resist and conduct offensive actions against us.”
Heavily armed MNLF forces entered the port city’s coastal neighbourhoods last Monday and took dozens of hostages in a bid to scupper peace talks between another rebel group and the government aimed at ending a decades-long rebellion in the south.
But Zagala said the fighting was concentrated in two coastal districts, while other areas were now secure.
Al Jazeera’s Jamela Alindogan, reporting from Zamboanga, said: “Up to now, the details on the ground remain sketchy.”
“There are text messages, peace observers have shown to me, from a hostage who said that the military has been directly or indirectly hitting civilians and hostages in between,” she said.
“What we know is, there are some 180 MLNF fighters and unknown number of hostages in the area, while human rights observers are trying to at least have a chance to get in and offer aid and medical assistance to the affected.”
Air and sea ports remained closed on Sunday in a crisis that has paralysed the city of one million, seen entire neighbourhoods razed to the ground, and forced tens of thousands to flee.
A ceasefire plan brokered by Jejomar Binay, Philippine vice president, and Nur Misuari, MNLF leader, was abandoned on Saturday after the two sides failed to agree terms.
The MNLF waged a 25-year guerrilla war for independence before signing a peace treaty in 1996 that granted limited self-rule to the south’s Muslim minority.
Misuari, who has accused the government of violating the terms of a 1996 treaty by negotiating a separate deal with a rival faction, had disappeared from public view shortly before the fighting began on Monday.
The rival faction, the Moro Islamic Liberation Front (MILF), is in the final stages of peace talks with Manila and is expected to take over an expanded autonomous Muslim region in the south by 2016.
President Benigno Aquino said the peace talks with the MILF aimed to end decades of rebellion that had claimed 150,000 lives in the country’s Muslim southern regions.