New approach for main stages of automatic controller tuning, process identification and controller parameters optimization, is proposed. It is based on methods of the three-stage estimation of a plant frequency response and on synthesis of a nonminimum phase transfer function using this response. For the above optimization, new criteria are introduced taking into account an influence of such processes non-linearities acted simultaneously as a backlash and a quantization with hysteresis. A proposed tuning procedure is illustrated by some examples of water level control systems at the IEC Power Boilers.