According to a first aspect, the invention relates to a method for controlling the navigation system of a carrier (P) receiving signals from a plurality of transmitters (T1-T3) and capable of measuring a pseudo-distance to each transmitter, wherein the elevation of each of the transmitters (T1-T3) is controlled relative to the horizontal (H) of the carrier (P), and a navigation solution is developed from the pseudo-distances (Pd-a) for which the elevation of the corresponding transmitter is higher than a minimum elevation (Em), characterized in that it comprises carrying out a discrimination of the multiple routes from the pseudo-distances (formula I) measured for the transmitters (T3) having an elevation lower than the minimum elevation (Em), and further retaining, during the development of the navigation solution, the pseudo-distances (Pd-ad) authorized after said discrimination. The invention also relates to a navigation system capable of implementing the method according to the first aspect of the invention.