In the paper, implementation of application specific logic controller for safety critical systems by means of Petri nets is described. The solution is based on duplicated main control unit and results comparison from both units. The design process of algorithm with use of Petri net is common for both unit. The hardware duplication is obtained during dual synthesis process. This process uses two different logic synthesis methods to obtain two different architectures for both control units. Such design flow simplify the process of realization of safety critical logic controllers.