A temperature estimation controller and methods are provided for controlling a torque command to prevent overheating of one or more of a plurality of phases of a permanent magnet motor. The temperature estimation controller includes a low speed temperature estimation module, a transition module and a temperature dependent torque command derater block. The low speed temperature estimation module determines a stator temperature of each of a plurality of phases of the permanent magnet motor in response to first thermal impedances measured for each of the plurality of phases with respect to a thermal neutral. The transition module is coupled to the low speed temperature estimation module and outputs the stator temperature of each of a plurality of phases of the permanent magnet motor as determined by the low speed temperature estimation module when a detected speed of the permanent magnet motor is less than a first predetermined speed. The temperature dependent torque command derater block is coupled to the transition module and derates the torque command in response to the stator temperature of one or more of the plurality of phases.