Officials said their efforts were made more difficult because the rebels were hiding among the civilian residents, and because they had failed so far to reach MNLF founder Nur Misuari.
Misuari had led the MNLF through a 25 year guerrilla war before signing a peace treaty with the government in 1996.
His faction later laid a similar deadly siege on Zamboanga in 2001 that led to his imprisonment until 2008, when all charges against him were dropped.
Misuari opposes a proposed government peace deal with rival rebel faction the Moro Islamic Liberation Front (MILF) aimed at ending the Muslim rebellion that had claimed 150,000 lives.
He has said that it would marginalise the MNLF and violate the terms of the 1996 peace deal.
The siege began four weeks after Misuari declared “independence” for the Muslim regions of the mainly Catholic nation and urged his followers to besiege government installations.
The military said the latest attack on Zamboanga is led by a top Misuari lieutenant, Habier Malik.
It has left 12 people dead and 36 wounded, according to the latest official tally.
The dead include eight rebels, two civilians, a police officer and a soldier. The wounded also included three policemen and 12 soldiers.
Zamboanga mayor Maria Isabelle Climaco Salazar told ABS CBN television that efforts from local government negotiators to convince Malik to free residents and leave the city had failed.
“They have tried to really reach out, to listen to what their demands are, but they refused to listen to anybody locally,” Salazar said.
Roxas said the gunmen were still using 80 “human shields”, down from 180 a day earlier. Salazar said some had escaped or been let go.
Absalom Cerveza, a Misuari spokesman, told ABS CBN the civilians “are not being used as shields” but fighters feared if they allowed them to leave the areas they could get caught in crossfire as they fled.
“We do not want to send them out for fear of their safety,” he said.
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