A chiller fault prediction system for a building, including one or more memory devices and one or more processors. The one or more memory devices are configured to store instructions to be executed on the one or more processors. The one or more processors are configured to receive chiller data for a plurality of chillers, the chiller data indicating performance of the plurality of chillers. The one or more processors are configured to generate, based on the received chiller data, a plurality of single chiller prediction models and a plurality of cluster chiller prediction models, the plurality of single chiller prediction models generated for each the plurality of chillers and the plurality of cluster chiller prediction models generated for chiller clusters of the plurality of chillers. The one or more processors are configured to label each of the plurality of single chiller prediction models and the plurality of cluster chiller prediction models as an accurately predicting chiller model or an inaccurately predicting chiller model based on a performance of each of the plurality of single chiller prediction models and a performance of each of the plurality of cluster chiller prediction models. The one or more processors are configured to predict a chiller fault with each of the plurality of single chiller prediction models labeled as the accurately predicting chiller models. The one or more processors are configured to predict a chiller fault for each of a plurality of assigned chillers assigned to one of a plurality of clusters labeled as the accurately predicting chiller model.