The work is devoted to the development of the control system for the specialized manipulator of the robotic mobile platform. The construction of the manipulator is considered and it's functioning when moving containers is described. The structure of the control system of the manipulator is developed and its subsystems are presented. The electrical scheme of the automaton for moving the rod with an electromagnet during loading and unloading of containers is proposed. A method of containers positioning when they are moved by a manipulator has been developed.