The 1st Army Region has been asked to explain alleged assaults on conscripts caught smoking marijuana in their barracks in Chon Buri, army chief Gen Narongphan Jitkaewtae said.
The conscripts complained they were beaten by their instructors last Friday.
Two came forward to lodge a police complaint. They said five conscripts were accused of smoking marijuana and beaten.
Both conscripts earlier showed wounds which they said occurred when instructors hit them and dragged them along a concrete floor. They also claimed instructors subjected them to waterboarding to make them confess.
On Tuesday, one conscript, Kajorn Prajong, 24, accompanied by his mother, Chatra Prajong, filed a complaint with police in Chon Buri accusing the instructors, whose names were not given, of assault.
The family had earlier told the government's Damrongtham complaint centre in Rayong about the incident.
Pvt Prajong submitted the result of his physical examination. He was later sent for another check-up at a local hospital. Local police will forward the investigation summary to the staff judge advocate for further legal proceedings.
Pvt Prajong reportedly admitted to have smoked marijuana in his sleeping quarters. However, the physical punishment he was receiving was too harsh and if he had not absconded from the barracks, he might have died, he said.
Gen Narongphan said he has ordered the 1st Army Region to explain the incident.
The facts must be divulged, the army chief said, adding the 1st Army Region has investigated and found the instructors who disciplined the conscript were also in the wrong. He did not elaborate.
Gen Narongphan said if the conscript in question had been caught smoking marijuana off-base he would have faced criminal punishment and possibly jailed.