In the paper, design flow of the application specific logic controllers with increased safety by means of Petri nets is proposed. The controller architecture is based on duplicated control unit and comparison results from both units. One specification of control algorithm is used by means of Petri net for both units. The hardware duplication is obtained during dual synthesis process. This process uses two different logic synthesis methods to obtain two different hardware configurations for both control units. Additionally, the dual verification is applied to increase reliability of the control algorithm. Such design flow simplifies the process of realization of control systems with increased safety.