Philippine forces were fighting Muslim rebels on two fronts Thursday as clashes broke out near a southern city being besieged by guerrillas opposed to peace talks with the government, officials said.

Moro National Liberation Front (MNLF) gunmen attacked army positions on Basilan island, wounding at least three soldiers, the military said.

Basilan is across a narrow strip of sea from Zamboanga, a major port city where about 180 MNLF fighters had been locked in sporadic clashes with troops since Monday, displacing about 13,000 residents.

"We would like to believe this is just part of their diversionary tactics," regional military spokesman Colonel Rodrigo Gregorio said of the Basilan attacks.

He said two other guerrilla groups with links to the MNLF were also involved in the fighting in Basilan, a jungle-clad island that is a traditional stronghold of the militants.

On the fourth day of the MNLF siege of Zamboanga, rebels fired mortars and snipers targeted government troops as they advanced on militant positions, an AFP reporter said.

The gunmen are followers of Nur Misuari, who founded the MNLF, which launched a long separatist rebellion in 1971.

He made a renewed declaration of "independence" a month ago after alleging the government was violating the terms of a 1996 peace deal that created a Muslim self-rule area in the south by negotiating a separate peace deal with a rival faction, the Moro Islamic Liberation Front (MILF).

Misuari has accused the government of reneging on its promises, and of sidelining his group in favour of the MILF, which is expected to take over an expanded autonomous region by 2016.

The government insists the proposed deal with the MILF would honour the MNLF agreement as it seeks to end an insurgency that has killed some 150,000 people in the south of the mainly Catholic nation.

The militants are hiding out among between 80 and 180 "human shields" in several neighbourhoods on the city's outskirts, officials said.

Social Welfare Secretary Corazon Soliman said Thursday that officials were trying to verify allegations that the gunmen had raped some of the women.

The alleged violations were reported by a resident who escaped from the gunmen, she added.

Gregorio said hundreds of elite soldiers backed by police had restricted the rebels' movement, but the presence of civilians was preventing any effort to end the siege by force.

Military spokesman Lieutenant Colonel Ramon Zagala added: "We cannot just conduct offensive actions without taking account of the hostages."

Apart from the three soldiers wounded in Basilan, one soldier was killed in a firefight with the rebels on Wednesday, when a village watchman who was mistaken for a guerrilla was fatally shot by the security forces, Gregorio said.

The killing raised the death toll during the standoff to 14, including three civilians, one police officer, two soldiers and eight rebels in four days of fighting.

Gregorio said two MNLF "stragglers" fleeing the area were also arrested Wednesday.

"Most members of the rank and file (of the MNLF) are already demoralised," he said.

Zamboanga Mayor Maria Isabelle Climaco Salazar said she finally managed to reach Misuari by telephone late Wednesday, and asked him to call off the siege.

She said Misuari told her he had given his followers on the ground "a free hand" in deciding their fate.

She said officials were moving to bring back vital services to the rest of the city of nearly one million, which has been paralysed by the siege.

She called on shops to re-open, doctors to remain in hospitals and for the public to remain calm as authorities established communication lines with rebel leaders to convince them to end the siege.

"I again (appeal) to the hostage takers, please let go of the hostages, especially the elderly, the sick, the children and people with disabilities," she said.

Meanwhile, officials called on residents who had been holding out in their homes in the conflict areas to leave and head for safety.