Many security techniques working at the physical layer need a correct channel state information (CSI) at the transmitter, especially when devices are equipped with multiple antennas. Therefore such techniques are vulnerable to pilot contamination attacks (PCAs) by which an attacker aims at inducing false CSI. In this paper we provide a solution to some PCA methods, by letting two legitimate parties to compare their channel estimates. The comparison is made in order to minimize the information leakage on the channel to a possible attacker. By reasonable assumptions on both the channel knowledge by the attacker and the correlation properties of the attacker and legitimate channels we show the validity of our solution. An accurate analysis of possible attacks and countermeasures is provided, together with a numerical evaluation of the attainable secrecy outage probability when our solution is used in conjunction with beamforming for secret communications.