Muslim villagers staged a protest Sunday morning, saying they did not believe Muslims were behind the attack.
More than 500 protesters gathered outside the school, carrying the dead children's bodies through the crowd and setting fire to two buildings at a nearby government-owned school. Some hurled stones at police.
"The villagers are accusing paratroopers of attacking the school," Thammasak said.
The latest violence comes after a Malaysian newspaper reported that a group of Thai Muslims crossed the border into Malaysia, complaining of harrassment by the Thai military.
The group of seven men and 17 women said they had been beaten and that family members were missing or detained, the Star said.
The Thai government installed after September's military coup says it is pursuing a policy of reconciliation to restore peace in the south, where separatist violence has killed 2,000 people since 2004.
A minibus attack that killed eight people last week has infuriated the Buddhist minority in the region and prompted authorities to increase security.