Four men dressed in similar uniforms to the Thai security forces sprayed bullets at a group of villagers gathered outside a local shop in Pattani province yesterday evening, said National Security Council chief Paradorn Pattanatabut.
"I deplore this act of brutality against civilians including children," he told AFP, adding one person had also been wounded in the attack.
He said the group responsible for yesterday's attack did not identify itself, but left a note saying the shooting was in revenge for the deaths of some of its members.
Buddhist and Muslims alike fall victim to the shadowy militants, who target security forces, civilians and perceived representatives of state authority such as teachers.
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Thailand held its first official peace talks with representatives of the Barisan Revolusi Nasional (BRN) in Malaysia in March and another round in April, but deadly attacks have continued.
Paradorn, who is Thailand's chief negotiator with the rebels, said meetings would go on, with more talks scheduled for June 13.
Leaflets apparently from a group linked to the BRN were also circulated in mosques, markets and tea shops in neighbouring Yala province early today pledging to continue murderous assaults on civilian targets.
Rebels involved in the talks on Sunday said they wanted "liberation" from Thailand.