In this work, a simple strategy for the development and implementation of a fault diagnosis system (FDS) that interacts with a schedule optimiser in batch chemical plants is presented. The proposed FDS consists of an artificial neural network (ANN) structure supplemented with a knowledge-based expert system (KBES) in a block-oriented configuration. The system combines the adaptive learning diagnostic procedure of the ANN and the transparent deep knowledge representation of the KBES. The information needed to implement the FDS includes a historical database of past batches, a Hazard and Operability (HAZOP) analysis and a model of the plant. Two motivating case studies are presented to show the results of the proposed methodology. The first corresponds to a fed-batch reactor. In this example, the FDS performance is demonstrated through the simulation of different process faults. The second case study corresponds to a multipurpose batch plant. In this case, the results of reactive scheduling are shown by simulating different abnormal situations. A performance comparison is made against the traditional scheduling approach without the support of the proposed FDS.