In this paper, the results of [7] are extended to the positioning of a high speed rotating shaft controlled via a magnetic suspension system, made up with four magnetic bearings. We recall the flatness based hierarchical control design of [6, 7] which allows us to distribute the roles of the electromagnets according to the current almost complementarity condition. Experimental results on a pilot vacuum pump of Alcatel/DTV are reported and comparisons with classical control schemes based on a tangent linear approximation are presented.