Concept Bottleneck Model (CBM) is a methods for explaining neural networks. In CBM, concepts which correspond to reasons of outputs are inserted in the last intermediate layer as observed values. It is expected that we can interpret the relationship between the output and concept similar to linear regression. However, this interpretation requires observing all concepts and decreases the generalization performance of neural networks. Partial CBM (PCBM), which uses partially observed concepts, has been devised to resolve these difficulties. Although some numerical experiments suggest that the generalization performance of PCBMs is almost as high as that of the original neural networks, the theoretical behavior of its generalization error has not been yet clarified since PCBM is singular statistical model. In this paper, we reveal the Bayesian generalization error in PCBM with a three-layered and linear architecture. The result indcates that the structure of partially observed concepts decreases the Bayesian generalization error compared with that of CBM (full-observed concepts).