From its inception, military intelligence suffered the greatest Possible antagonism from the Tchekists. The Tcheka had its own central agent network and an agent network in local areas. The Tchekists jealously guarded their right to have secret agents and could not resign themselves to the idea that anyone else was operating similar secret networks. The Tcheka also had units of 'special assignments' which carried out raids, not in the enemy's rear, but in its own rear, destroying those who were dissatisfied with the communist order.

During the civil war the Tcheka strove to unite all special assignment units under its own control. Several cases are recorded of the Tchekists trying to take over organs of military intelligence. One such attempt occurred on 10 July 1918 when the Tcheka shot the whole staff of the Eastern Front intelligence department, which had been in existence for only twenty-seven days, together with the entire staff of the front and the commander himself, M. A. Muravev, who had been trying to intervene in favour of his intelligence department. The whole of the agent system of military intelligence passed into the control of the Tchekists, but this brought the front to the very edge of catastrophe. The new commander, I. I. Vatsetis, and his chief of staff had no intelligence service of their own, and were unable to ask for the necessary information. They could only request information in a very tactful way, being well aware of the Tcheka's attitude to those it disliked. (As regards Vatsetis the Tchekists did indeed shoot him, but much later.)

Naturally while the agent network was under the control of the Tcheka, its own work was given priority, and any tasks set it by the Army Command were given very low priority.