MANILA -- Two small, ultraviolent rebel groups joined forces to fight government troops Thursday in the southern Philippines, in a clash that occurred on an island adjacent to the city where several hundred rebels are in a standoff with the Philippine military.
The violence raised fears of a widening of the insurgent threat in the area, where the government has for decades been struggling to contain attacks by Muslim-led groups.
Three soldiers were wounded in the firefight, which occurred at 9:30 a.m. in the village of Lamitan on the restive southern Philippine island of Basilan, according to a statement from the Philippine military. Basilan government officials told a local radio station that five people from the area were missing after the attack.
The attack involved combined forces of the Abu Sayyaf Group, which has engaged in kidnappings and beheadings in the area for more than a decade, and the recently formed Bangsamoro Islamic Freedom Fighters, a violent offshoot of a larger rebel group.
"According to our sources, the two groups have formed an alliance," Col. Rodrigo Gregorio, a military spokesman in the area, said by telephone Thursday.
He said the Basilan battle, which involved about 150 rebels, did not appear to be a widening of the conflict in nearby Zamboanga City, where a faction of the Moro National Liberation Front has been holding dozens of hostages, virtually paralyzing the important trading area.
"There is no connection to the situation in Zamboanga City," said Colonel Gregorio, adding that Abu Sayyaf is active on Basilan and periodically stages attacks. "We are in hot pursuit of them now," he said.
National government officials have said they are seeking a peaceful resolution to the standoff in Zamboanga City, but on Thursday a presidential spokesman, Edwin Lacierda, said the use of force remained an option in light of the attack on Basilan.
"The forces of the state are ready to exercise the resolve of the government," Mr. Lacierda said in a statement. "While the government is exhausting all avenues for a peaceful resolution to the situation, let it be clear to those defying us that they should not entertain the illusion that the state will hesitate to use its forces to protect our people."
On Thursday afternoon, a plume of black smoke could be seen pouring from the rebel-held area in Zamboanga City. Local officials said a blaze had raged out of control because firefighters, concerned about sniper fire, could not enter the area.
Sporadic gunfire could be heard in the rebel areas. All commercial flights into the city remained canceled. Philippine Air Force transport planes were used to fly stranded passengers to nearby Cebu City to catch flights. City government officials warned against bus travel into Zamboanga, noting that the national highway was not secured. More than 15,000 residents have been evacuated or have fled the area because of the standoff, officials said.
It remained unclear who was leading the group of about 300 armed men holding off military forces in Zamboanga City.
Nur Misuari, the founding chairman of the Moro National Liberation Front, told officials on Thursday that a breakaway faction led by Habier Malik, a rebel leader, had taken action in Zamboanga City, and not the main rebel group with which Mr. Misuari is affiliated.
"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," Beng Climaco, the mayor of Zamboanga City, said on Thursday. "Misuari disowned the actions of Habier Malik, the leader of the hostage takers, with whom I communicated separately."
Some military leaders were skeptical of Mr. Misuari's claim. "Nur Misuari is denying his involvement, but all indications point to his running this operation in Zamboanga City from the very beginning," Colonel Gregorio said.
The conflict in Zamboanga City began Monday when several hundred heavily armed men tried to march to City Hall to raise a flag and declare independence from the national government, according to the police. The rebels claim that it was a peaceful march and that they were attacked by the military.
The group has demanded that the Organization of Islamic Cooperation or the United Nations be brought in to facilitate negotiations, according to Mayor Climaco. The national government has countered that the standoff is a domestic matter.
The Moro National Liberation Front signed a peace deal with the Philippine government in 1996, but its leaders were angered when a separate agreement was forged with the rival Moro Islamic Liberation Front last year that some leaders said would encroach on the original deal.
The Abu Sayyaf Group and the Bangsamoro Islamic Freedom fighters did not participate in peace talks, and they advocate an armed struggle to establish an Islamic state in the southern Philippines. Security analysts say Abu Sayyaf has lost much of its ideological underpinnings and operates primarily as a kidnap-for-ransom gang.
Correction: September 12, 2013, Thursday
This article has been revised to reflect the following correction: Due to an editing error, an earlier version of this article incorrectly referred to Mayor Beng Climaco of Zamboanga City on second reference as "Mr." Mayor Climaco is a woman.
This article originally appeared in The New York Times.