Recently, there has been an increasing need for development of active magnetic bearing (AMB) systems of smaller size and lower energy consumption than ever, as AMBs seek for applications in compact, portable rotating machines such as hard disk spindle and artificial heart blood pump. Among others, the three-pole AMB configuration turns out to be more profitable in terms of compactness in design and low power loss than the conventional four-or eight-pole AMB. However, one of the inherent drawbacks in controller design of three-pole AMB is the strong coupling in magnetic flux between magnetic poles. It leads to the strongly non-linear system behavior, when the equation of motion is formulated in the conventional Cartesian coordinates. In this paper, we propose use of the redundant bearing coordinates to describe the three-pole AMB system behavior, so that the potential difference controllers can be easily designed, based on the decoupled linearized control model for each pole. The proposed method is applied to control of a five-axis AMB system, which consists of a three-pole radial AMB for stabilization in the radial direction and a ring-type permanent magnet bearing for levitation in the axial and tilt directions. It is shown that simplistic equation of motion for the five-axis AMB system can be derived in the proposed redundant bearing coordinates and the resulting control equations become completely decoupled. Experiments are also carried out with the five-axis disk-type AMB system equipped with Hall diodes for measurement of the radial displacement and it is confirmed that the proposed control scheme succeeds in the run-up test.