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The makeshift device exploded as troops passed by in a pick up truck on a busy street in Yala, one of three provinces near the Malaysian border that have been under emergency rule since 2005.
Civilians were among the casualties, police said.
Yala governer Krissada Boonraj said the perpetrators had waited until after the long holiday weekend for Thai New Year to plant the bomb.
"The insurgents were waiting to attack after Songkran as during that time we were strictly controlling the situation," he said.