The body of Matohlafi Maesae, a district official in Narathiwat Province which borders Malaysia, was found on a roadside on Saturday, three days after he was reportedly abducted from his home by armed men.
Narathiwat's Islamic council chairman, Abd al-Rahman Abd a-l Samad, said Muslims were alarmed, and believed Matohlafi had been murdered by officials who suspected he was involved in separatist groups and the 4 January raid on an arms depot.
"They are very concerned and frightened. They believe men in uniform are involved with the kidnapping," Abd al-Rahman said.
"They're afraid they will be the next to be kidnapped or killed," he said, adding that residents were staying behind closed doors after dark.
Abd al-Rahman said he and the chairmen of the Islamic councils of the other four provinces in the deep south hoped to petition Prime Minister Thaksin Shinawatra to look into the killing.
"They (Muslims) are very concerned and frightened. They're afraid they will be the next to be kidnapped or killed"
Abd al-Rahman Abd al-Samad,
Muslim-majority in southern Thailand, where a low-grade separatist movement has simmered for decades, has been gripped by a sudden wave of unrest this month.
The arms depot raid left four soldiers dead while 18 schools were set ablaze in a coordinated attack.
The following day, a bomb blast in neighbouring Pattani killed two soldiers, while gunmen attacked a Yala province police station on 6 January, injuring two policemen.
The Bangkok Post quoted Matohlafi's relatives as saying his body bore marks of torture, and that 10 marines visited his home in Bacho district shortly after the abduction, claiming to be looking for something.
Police were investigating the death and believed it to be tied to personal conflicts or robbery, Bachao police Colonel Wana Awapak said.
Meanwhile, the commander in charge of military operations in the region, parts of which are under martial law, said the taskforces conducting the hunt for those responsible for the string of violence would remain in place.
Thai authorities have arrested one man over the Yala police
station attack, and another reportedly has been arrested over the arms depot raid. Warrants have been issued for at least 11 people.