(CNN) -- Sporadic and intermittent gunfire rang out in Zamboanga City for a fourth day on Thursday as armed forces continued to clash with Muslim Moro National Liberation Front rebels holding as many as 180 hostages on the Philippine island of Mindanao.
Lt. Colonel Ramon Zagala, spokesman for the Philippines Armed Forces (AFP), told CNN that government troops currently had "contained" an estimated 180 MNLF rebels in five districts of the mainly Christian city.
"Right now we went to ensure that we keep them in those locations so they can't get in and they can't get out," he said. "But unfortunately they are holding between 160 and 180 hostages."
He said their original plan had been to land by sea and march on Zamboanga's city hall and raise the MNLF flag.
"We stopped that but now our immediate concern is the safety and the security of the hostages," Zagala said, adding that Philippines troops were under orders to contain the rebels and were not engaged in what he called "offensive operations."
He said the intermittent gunfire that could be heard across the city was a part of the containment operation.
"Sometimes these elements (rebels) are trying to punch out and they fire at us so we also fire at them," Zagala said. He said the condition of the hostages was not known, but crisis managers were concerned about a lack of food and water.
Zagala said rebels had killed two government troops -- one during the first encounter at sea and the second was killed by sniper fire on Tuesday -- and wounded 17 more.
AFP forces had recovered one rebel body.
"We can't verify the rebel body count because we don't have the bodies but the best figure that we have is that AFP has killed 14 MNLF," he said.
Almost 13,000 people have been evacuated from the districts of Talon-Talon, Santa Barbara, Santa Catalina, Kasanyangan, Canela and Mampang in Zamboanga, government sources said.
Zamboanga's mayor, Isabelle Climaco Salazar, told a press briefing that she had been in direct contact with the head of the MNLF rebels, Nur Misuari, and the leader of the hostage takers, Habier Malik.
"Last night I was able to talk to Chairman Nur Misuari hoping that it would pave the way for the peaceful end of this crisis," Climaco said. "What is of interest is that Misuari disowned the actions of Habier Malik, the leader of the hostage-takers with whom I communicated separately."
Zagala said that while Misuari had disavowed the actions of Malik, saying that the commanders in the MNLF were free to carry out actions as they wished, he said it was the government's belief that Misuari was behind the current rebel action.
The MNLF, a separatist movement founded in 1971 by Nur Misuari with the aim of establishing an autonomous region for Muslims in this mainly Catholic country, signed a peace deal with the central government in Manila in 1996, though some of its members have broken away to continue a violent campaign.
Last month, Misuari issued a "declaration of independence" for the Moro nation -- referring to Mindanao's indigenous Muslim population -- after complaining that the MNLF had been left out of a recent wealth-sharing agreement with another insurgent group, the Moro Islamic Liberation Front, or MILF, which has fought for decades to set up an independent Islamic state on the resource-rich island of Mindanao.
Under the agreement signed this year, Muslims will get a 75% share of income derived from the exploitation of metallic minerals in the area -- reported to include gold and copper. The current stand-off is believed to be linked to the terms of the agreement.
Philippine President Benigno Aquino's plan is to achieve lasting peace in the region by 2016 when his term ends.
Agreements have yet to be reached on power-sharing and normalization, which means giving up arms. A report published last year by the International Crisis Group warned that the peace process needed to find ways to support insurgents as they build normal, civilian lives.