Four others were wounded when a ranger unit opened fire on their pickup truck in Nongchik district of Pattani province.
The military ordered the withdrawal of the unit immediately after the incident and set up a panel including a local religious leader to investigate.
"The incident in which on-duty security officials acted against civilians was likely caused by a misunderstanding resulting from the surrounding circumstances," the statement from the southern region army command said.
It said the incident occurred as troops were in pursuit of militants who had attacked a ranger outpost, adding that it was up to the Thai judiciary to establish the guilt of the rangers, irrespective of the findings of the panel.
"All those who are involved with the incident will enter the justice process to ensure confidence and fairness from all sides," the statement said.
A complex insurgency, without clearly stated aims, has plagued Thailand's far south near the border with Malaysia since 2004, claiming more than 5,000 lives, both Buddhist and Muslim, in near-daily bomb or gun attacks.
In the latest violence, a ranger was killed in a roadside bomb attack early Wednesday in Cho-Ai-Rong district of Narathiwat province, police said. Three others including two rangers and a villager were wounded.
The five kilogram (11 pound) bomb was hidden at the foot of a bridge and detonated by radio control after villagers alerted rangers about the suspicious object, police said.