Lt. Col. Ramon Zagala, spokesman for the Armed Forces of the Philippines, said as much as 80 percent of the areas previously controlled by the rebels were now in government hands, the Philippines News Agency reported.
"We are currently pushing forward and in the areas we have recaptured, we have already started our clearing operations," he said, adding there had been no major incidents in the past 24 hours.
A faction of the Moro National Liberation Front, identified as the Nur Misuari-led faction, attacked the largely Christian southern port city Sept. 9. The military was later called in as the rebels took control of several of the city's villages, leading to a standoff that left dozens, mostly rebels, dead.
Authorities said the rebels also took dozens of civilians hostage, using some of them as human shields in gunfights with the military. Many of the hostages were subsequently released.
ABS-CBN reported some renewed fighting Wednesday and fires in the conflict zone, including the village of Santa Catalina.
The report quoted Zagala as saying the military is implementing a gradual constriction in the conflict areas to root out the rebels and rescue the hostages.
In other developments, local police chief Jose Malayo, reportedly abducted by the rebels while conducting negotiations, has since been released along with 23 hostages, other reports said. ABS-CBN said the identities of the 23 were being verified.