An army spokesman said on Wednesday that militants staged attacks in Yala late on Tuesday, taking M-16 rifles and shotguns from checkpoints manned by civil defense volunteers.
“Twelve were killed at the scene, two more [died] at the hospital, and one died this morning,” he said.
The areas surrounding the checkpoints were closed off by security forces as experts carried out forensic investigations, he added.
Militants seeking greater autonomy in southern Thailand have been fighting Thai forces for years.
Three provinces in the south, namely Yala, Pattani, and Narathiwat, have faced militancy since 2004.
According to sources monitoring the conflict, more than 7,000 people have so far lost their lives in the violence over the last 15 years.
Militants often target perceived collaborators with the Thai government. Muslims and Buddhist civilians have fallen victim to their shooting or bomb attacks.
The Thai junta, which seized power in 2014, has held several rounds of talks with one group that claims to represent the militants, Mara Patani. But the talks have failed to make headway so far, and many doubt the negotiators have any sway over militants on the ground.