The aim of the method of controlling at least one mechanical system exhibiting at least one flexible structure element and at least one actuator or group of actuators is to reduce the level of vibrations of said element while controlling the actuator or group of actuators in such a way as to achieve at least one objective assigned to the mechanical system. The control consists of increments having to be carried out at a sampling period T, each of the increments being constant in amplitude in a sampling time interval extending between two successive sampling instants and each of the increments being applied during a duration which is less than or equal to the sampling period T. In each sampling interval, at least one of the initial and final instants of application of the increment is modified by adding a variable, random or pseudo-random, temporal deviation dT.