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Static offset and synchronous vibration are obstacles to precision tracking of a rotating shaft supported by active magnetic bearings (AMBs). A constant and harmonic disturbance observer is an effective approach to estimate and suppress these undesired effects. A disturbance observer is particularly well-suited for tracking applications since it can directly compensate for AMB force nonlinearity. In this paper, we propose a nonlinear reduced-order disturbance observer which is incorporated into a flatness-based tracking control. Since a reduced-order approach requires knowledge of velocity, we design an inner-loop velocity observer which can achieve convergence at a faster rate than the disturbance observer. This hierarchical observer simplifies the control because disturbance estimates are decoupled for each degree of freedom (DOF) and disturbance compensation is modularized. Experimental results on a commercially available 5-DOF system demonstrate accurate position tracking over the bearing air gap for a wide range of shaft velocities.