Mamasapano town mayor Benzar Ampatuan said residents had told him police tied up the man to stop him tipping off their targets ahead of the pre-dawn raid, in which 44 commandos died in one of the force's bloodiest days in recent years.
A local farmer's daughter and two other men were also found dead in their homes after the fighting, Ampatuan said, the first report of civilian casualties in the bloodbath.
The Philippines yesterday held a national day of mourning for the dead police officers, who were killed as they hunted the man blamed for the 2002 Bali bombings in Indonesia, in which 202 people died.
Nearly 400 members of the elite police unit were sent to a village near the town of Mamasapano on January 25 to arrest Zulkifli bin Hir alias Marwan.
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The Moro Islamic Liberation Front (MILF) said 11 of its fighters were killed and 15 wounded in the gunfight that ensued. A second rebel force, the MILF splinter group Bangsamoro Islamic Freedom Fighters, has not disclosed whether it suffered any casualties.
The government has faced calls for retribution after at least one police survivor alleged some of the policemen were killed after they surrendered and their corpses were desecrated.
Despite the bloodbath, both the Philippine government and the MILF pledged at the end of the Kuala Lumpur talks today to pursue their 2014 agreement.
The process calls on parliament to pass a law giving minority Muslims self-rule over several provinces and for the 10,000-member MILF to disarm gradually.