An apparatus for controlling a multi-winding rotary machine including an armature formed of a plurality of winding sets. In the apparatus, a command voltage calculator calculates command voltages to be applied to each winding set so as to control currents detected by a current detector to their respectively corresponding command currents. An interfering voltage calculator calculates, for each of the winding sets, interfering voltages proportional to the rotation speed of the rotary machine. An interfering voltage compensator compensates, for each of the winding sets, the command voltages for their respectively corresponding interfering voltages. An operation unit operates a voltage applicator to apply output values of the interfering voltage compensator to each winding set.