Manufacturing control systems are facing difficulty on adopting agility in today's dynamic environment. Much research has been conducted on the use of multi-agent systems to facilitate this transition. In our previous work, a radio frequency identification-enabled multi-agent-based manufacturing control system was introduced for flexible manufacturing systems. In that control system, a direct coordination mechanism coordinates the agents. However, the decision-making response of the control system to disturbances was low and caused the agents to spend more time on processing messages than doing the actual job. Thus, in this article, we propose an indirect coordination mechanism based on ant colony intelligence aiming to improve the self-organization and processing time of the system. The new system utilizes the stigmergy mechanism for cooperation among the agents. Furthermore, ant agents are created by the existing agents to enable communication among them. The proposed new mechanism was implemented in a flexible assembly line. The simulation results of a case study considering shop floor problems indicates, for most performance measures, that the radio frequency identification-enabled multi-agent-based manufacturing control system integrated with indirect coordination mechanism performs better in comparison with the radio frequency identification-enabled multi-agent-based manufacturing control system integrated with direct coordination mechanism.