A control system for autopilot transport robots in warehouses has been developed to solve the problem of transportation, loading and unloading of the merchandise. The system is implemented on the basis of an organizational model of the mobile robots control process using a multi-agent approach. The proposed model describes the interaction of agents, the functions and the amount of work they perform, as well as the set of admissible states. Implemented an algorithm for finding the shortest path in the virtual world of a warehouse to find needed targets. The developed system effectiveness has been demonstrated using computer simulations and experiments.