President Benigno Aquino III flew to Zamboanga earlier Friday to visit government troops and some of the 24,000 residents displaced by the violence. He warned in a speech that his government won't hesitate to use force to end the most serious security crisis his administration has faced since he came to power in 2010.
There was also fighting on Friday, and ABS-CBN TV reported that voices presumably of hostages were heard shouting "cease fire, cease fire." One government soldier was reportedly wounded.
The Moro National Liberation Front rebels have been overshadowed by a rival group in talks with the government for a new minority Muslim autonomy deal.
Misuari signed a peace deal in 1996, but the guerrillas did not lay down their arms and later accused the government of reneging on a promise to develop long-neglected Muslim regions in the predominantly Roman Catholic nation. The government says Misuari kept on stalling and making new demands.
Misuari has not been seen in public since the standoff began.
"There are lines they should not cross," Aquino said of the rebels. He said the government would be obligated to use "the force of the state" if those lines are crossed.
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Associated Press writer Jim Gomez in Manila contributed to this report.