The rebels, suspected members of a faction of the Moro National Liberation Front, were believed to be hiding in the villages of the largely-Christian Zamboanaga City, and were reported to be holding hostages, using some of them as "human shields," as they fight government troops. The violence, which began Monday, reportedly has already claimed six lives, although a handful of hostages had been released as negotiations continued.
ABS-CBN news.com reported gunfights erupted early Wednesday in the villages of Santa Barbara and Santa Catalina and continued for about three hours. There were no immediate reports of casualties.
Those two villages along with Talon-talon, Mampang and Kasanyangan were reported to be the worst affected by the violence.
Zamboanga City is on the southern coast of Mindanao, the southernmost island in the Philippines which has been the scene of Muslim separatist violence in the past.
The Voice of America quoted officials who said a faction of more than 200 fighters led by an MNLF commander had planned to raise a separatist flag in Zamboanga City hall, but were intercepted by security forces.
The number of residents who have fled their homes since the rebels came into the city had topped 6,000, ABS-CBN reported. Most of them have been housed in the city's Joaquin F. Enriquez Memorial Sports Complex. A city councilor said the evacuees need additional supplies of food and other necessary items including clothes and infant formula.
Maria Isabelle Climaco-Salazar, mayor of the port city, earlier said about 170 civilians were still being held hostage by members of the Nur Misuari-led faction of the MNLF. Local authorities said the rebels were using some of the hostages as "human shields," ABS-CBN reported.
Lt. Col. Ramon Zagala, spokesman for the Armed Forces of the Philippines, said Wednesday the troops were "standing down to allow crisis management committee to make necessary moves to resolve-negotiate peacefully," the Philippines News Agency reported. He said there is no ceasefire with the rebels.
"There is no formal ceasefire contrary to some reports," Zagala said, adding it is the rebels who should first leave the city.
On Tuesday, Philippines President Benigno S. Aquino III said the government would ensure security forces in Zamboanga City are beefed up to maintain order and protect the citizens, the government web site reported. He also said there was no need to declare a state of emergency in the province since the current operations were being handled by the combined personnel of the Armed Forces of the Philippines and the Philippine National Police.
The country's civil aviation authorities extended their declaration of the city as a "no fly zone" until Thursday, PNA said.
ABS-CBN quoted officials who said negotiators were trying to contact one of the leaders of the hostage-takers, identified as Ustadz Habier Malik.
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.
Notable deaths of 2014 [PHOTOS]