The standoff between fighters of a Nur Misuari-led faction of the Moro National Liberation Front began Sept. 9, with about 200 people being held hostage by the rebels, Voice of America reported.
Armed Forces spokesman Brig. Gen. Domingo Tutaan said 195 hostages have been freed and security forces will remain in the area to search for rebels.
"So it's really clearing in the strict sense of it, of any member of the Misuari faction, who are probably hiding or holed out in the area, avoiding or trying to elude arrest," he said.
The standoff caused more than $4.6 million worth of damage to Zamboanga and thousands of residents were displaced during the fighting, ABS-CBNnews.com reported.
"The fighting might be over, but the crisis continues on as we have to face reality hence forward," Zamboanga Mayor Beng Climaco said Saturday.
Climaco said the army's clearing operation will likely take about two weeks.
She thanked police and military forces "who are at the forefront trying to keep Zamboanga safe."
At least 15 soldiers were killed during the standoff, while 183 rebels were killed and 292 others are in custody.
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