The rebels, identified as members of the Nur Misuari-led faction of the Moro Liberation Front, have been holed up since last week in the largely Christian Zamboanga City on the country's southern-most Mindanao Island, apparently with the aim of taking over the city. The rebels had taken dozens of local people hostage before freeing some of them. A cease fire announced over the weekend did not take hold.
Lt. Col. Ramon Zagala, spokesman for the Armed Forces of the Philippines, told a television channel: "We now believe that they are not an organized force anymore and a lot of them are fleeing. The momentum belongs to the (armed forces)," the Philippine Star reported.
He said 51 rebels have been killed and another 48 had either surrendered or been captured.
The military also had seized arms and ammunition.
"We continue to push forward and that we are now constricting this MNLF-Misuari faction so that we can eventually put an end to this crisis at the soonest time possible," Zagala said.
The report said besides the rebels, at least a dozen civilians had been killed, while another 105 people, including 23 civilians, have been injured.
The standoff has resulted in about 60,000 people being evacuated.
Zagala said the military is still open to a cease fire with the rebels, but added such a step is not possible "if they do not stop their offensive actions or their attacks against the [military] members and the civilians."
ABS-CBN reported rebel snipers began firing at high-rise buildings Monday in the port city's Santa Catalina village after they noticed some residents in those buildings watching the standoff.
The report said both the military and the rebels were using mortars as fighting resumed Monday.
Philippine President Benigno S. Aquino III and officials accompanying him remained in Zamboanga City for the third day Sunday, the Daily Inquirer reported. A presidential spokesman was quoted as saying days of negotiations with the rebels had failed, leaving the government no option but to launch a military operation.
The government has said the rebels were using their hostages as human shield in some of the villages.
The MNLF, founded in 1971, has sought an autonomous region for the Muslims in the country. The group signed a peace deal with the Philippines government in 1996 but some of its members have since broken away from the group to continue its campaign.
President Aquino last week warned the rebels will face military force if there is increased threat to civilians.
"There are lines that they cannot cross. If they cross those lines, we will be obligated to use the state's force against them," CNN quoted him as saying.
The report said Misuari last month issued a "declaration of independence" for Mindanao's Muslim population. He said the MNLF was not included in a recent wealth-sharing agreement with another insurgent group.