Since the damage from cyber-attacks increases, there is an urgent need to research and develop security countermeasures for control systems. In the control system, the controller is an important device. This paper then considers a whitelisting system that models the normal operation sequence of a PLC (Programmable Logic Controller) and detects deviations from the model as abnormal. We propose three methods to auto-generate the whitelisting system by LD (Ladder Diagram): Petri net model generation, constraint condition derivation, and LD conversion. The first method generates Petri net models form SFCs (Sequential Function Charts) that are compatible with LDs. The second method derives whitelist conditions from Petri net models to check whether PLC performs the correct operation sequence. The third method implements the whitelist conditions into LD. The auto-generated whitelisting system enables us to monitor the state transitions of the PLC programs. Further, this paper carries out an experimental validation of the methods using a testbed system.