Magnetic components significantly contribute to the dissipated loss in power electronic converters. Measuring the true value of dissipated power in these components is highly desirable, since it can be used to verify the optimum design of these components. The common approach for measuring the loss in magnetic cores is B-H loop measurement where two windings are placed on the core under test. However, this method is highly vulnerable to phase shift error, especially for low-permeability, low-loss cores. Due to soft saturation and very low core loss, low-permeability low-loss magnetic cores are favorable in many of the high-efficiency high power-density power converters. Magnetic powder cores, among the low-permeability low-loss cores, are very attractive since they possess lower magnetic losses in compared to gapped ferrites. This paper presents an analytical study of the phase shift error in the core loss measuring of low-permeability, low-loss magnetic cores. Furthermore, the susceptibility of this measurement approach has been analytically investigated under different excitations. It has been shown that this method, under square-wave excitation, is more accurate compared to sinusoidal excitation. The analysis has been validated by experimental measurements for relatively low-loss magnetic cores with different permeability values.