Pilot contamination (PC) is a well-known problem that affects massive multiple-input multiple-output (MIMO) systems. When frequency and pilots are reused between different cells, PC constitutes one of the main bottlenecks of the system's performance. In this paper, we propose a method based on the variational autoencoder (VAE), capable of reducing the impact of PC-related interference during channel estimation (CE). We obtain the first and second-order statistics of the conditionally Gaussian (CG) channels for both the user equipments (UEs) in a cell of interest and those in interfering cells, and we then use these moments to compute conditional linear minimum mean square error estimates. We show that the proposed estimator is capable of exploiting the interferers' additional statistical knowledge, outperforming other classical approaches. Moreover, we highlight how the achievable performance is tied to the chosen setup, making the setup selection crucial in the study of multi-cell CE.