The present invention relates to a method of decoupling the mode of automatic following of the lateral profile and the mode of automatic following of the vertical profile of an automatic guidance system of an aircraft (A) flying on a reference trajectory (T). The mode of automatic following of the vertical profile is not disengaged immediately on disengaging the mode of automatic following of the lateral profile. After disengaging the mode of automatic following of the lateral profile, the mode of automatic following of the vertical profile is disengaged automatically only if at least one criterion of lateral separation between the current or short-term position of the aircraft and the lateral profile corresponding to the reference trajectory is satisfied, having regard to the position error.