Modern healthcare systems knitted by a web of entities (e.g., hospitals, clinics, pharmacy companies) are collecting a huge volume of healthcare data from a large number of individuals with all sorts of medical procedures, medications, diagnosis, lab tests, and so on. To extract meaningful medical concepts (i.e., phenotypes) from such higher-arity relational healthcare data, tensor factorization has been proven to be an effective approach and received increasing research attention, due to their intrinsic capability to accommodate the high-dimensional data and provide adequate representation power. Recently, federated learning offers a privacy-preserving paradigm for collaborative learning among different entities, which seemingly provides an ideal potential to further enhance the tensor factorization-based collaborative phenotyping to handle sensitive personal health data. However, existing attempts to federated tensor factorization come with various limitations, e.g., restricted to the classic tensor factorization, high communication cost, and reduced accuracy. We propose a communication-efficient federated generalized tensor factorization, which is flexible enough to choose from a variate of losses to best suit different types of data in practice. We design a three-level communication reduction strategy tailored to the generalized tensor factorization, which is able to reduce the uplink communication cost up to 99.90%. In addition, we theoretically prove that our algorithm does not compromise convergence speed despite the aggressive communication compression. Extensive experiments on two real-world electronics health record datasets demonstrate the efficiency improvements in terms of computation and communication cost.