A soldier killed in a firefight with the rebels in Zamboanga and a village watchman who was mistaken for a guerrilla and shot dead by the security forces, both on Wednesday, were among the other fresh fatalities.
Social Welfare Secretary Corazon Soliman said Thursday that officials were trying to verify allegations that the gunmen had raped some of the local women.
About 13,000 people fled to a sports complex, as aid agencies called for a humanitarian corridor for those still trapped.
The mayor 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 stay calm as authorities seek to convince the rebels to leave.
Officials also called on the remaining residents in the conflict areas to leave their homes and head for safety.
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