Operation management and equipment control of plants are carried out based on measurements obtained from flowmeters installed in the plants. Therefore, it is necessary to always observe the flowmeters to detect and diagnose faults, and to correct measurements. However, the fault of the flowmeters, such as bias of the indicated value, can be repaired only during regular maintenance under present circumstances. If the flowmeters with bias of the indicated value can be detected beforehand, reasonable repair plans can be planned. In addition, the bias can be corrected during normal plant operation. A fault diagnosis method using historical database is developed for the flowmeters installed in the plant where the state of the plant always changes by influence of load fluctuation. In the previous study, a design method of the fault diagnosis system that can satisfy specifications required from users about probabilities of a miss-diagnosis and an incorrect-diagnosis is developed. This study proposes a new design and pre-evaluation method based on probabilities of a false-alarm and a miss-alarm, which are more important evaluation criteria. The effectiveness of this method is demonstrated by using Monte Carlo simulations of a tank-pipeline system.