Federated learning has a significant advantage in protecting information privacy. Many scholars proposed various secure learning methods within the framework of federated learning but the study on secure federated unsupervised learning especially clustering is limited. We in this work propose a secure kernelized factorization method for federated spectral clustering on distributed dataset. The method is non-trivial because the kernel or similarity matrix for spectral clustering is computed by data pairs, which violates the principle of privacy protection. Our method implicitly constructs an approximation for the kernel matrix on distributed data such that we can perform spectral clustering under the constraint of privacy protection. We provide a convergence guarantee of the optimization algorithm, reconstruction error bounds of the Gaussian kernel matrix, and the sufficient condition of correct clustering of our method. We also present some results of differential privacy. Numerical results on synthetic and real datasets demonstrate that the proposed method is efficient and accurate in comparison to the baselines.