Lt Gen Seehanat Wongsarote, chief of the Directorate of Joint Intelligence, made the comment after visiting Col Witthavas Wattanakul in hospital on Friday.
Col Witthavas suffered serious wounds to his legs and body after being attacked by People's Democratic Reform Committee (PDRC) guards on Thursday night.
He told Thung Song Hong police that the attack took place as he stepped out of his car to move traffic cones that were blocking the traffic on on Chaeng Watthana Road as he was returning to his flat at Muang Thong Thani from a restaurant in the Sukhumvit area.
He was later taken Mongkutwattana General Hospital after the guards realised that he was a soldier.
The area is controlled by the PDRC faction led by the hardline monk Luang Pu Buddha Isara.
One of the guard leaders, whose name was not released, visited the soldier and apologised, saying that his guards had misunderstood and thought he was entering the area to confront protesters.
Supreme Commander Gen Tanasak Patimaprakorn ordered subordinators to coordinate with the protest faction ito ensure the safety of officers working at the Supreme Command which is in the area blocked by the protesters.