Philippines government forces have clashed repeatedly this week with Muslim rebels holding more than 100 hostages in the southern port city of Zamboanga.
Area residents fled on Thursday as government troops attempted to drive rebel fighters from parts of the city, and houses were set on fire amid the violence.
Meanwhile an unidentified group of gunmen separately attacked another town on Basilan island, local media reported.
The Philippine government has warned Muslim rebels to end peacefully the standoff as soon as possible.
Edwin Lacierda, a presidential spokesman, said Thursday that any attempts by other groups to start trouble would be crushed, citing the army's thwarting of an armed group's attempt to set a nearby village and wharf on fire.
"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," Lacierda said.
"It is time for you to cooperate to resolve this situation peacefully at the soonest possible time."
The Moro National Liberation Front (MNLF) signed a 1996 peace accord with the government, but many of its fighters have held on to their weapons and accused officials of reneging on a promise to develop an autonomous region for minority Muslims in the south of the predominantly Roman Catholic Philippines.
The group has said it was being left out in government's negotiations with another fighter group, the Moro Islamic Liberation Front, which broke away from the MNLF in the early 1980s.
Al Jazeera and wire services
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