Displaying non-minimum phase transient response in the impedance circuit of three-phase Z-source inverters places a fundamental restriction on the achievable performance of this class of converters. In this paper, an internal model control (IMC) has been proposed in order to rectify the significant phase lag caused by the right half-plane (RHP) zero of the dc-side capacitor voltage to the shoot-through transfer function. The basic one-degree of freedom structure of IMC is an alternative to conventional feedback controllers; IMC is able to cancel the non-minimum phase effects and can satisfy the desired phase margin. An IMC is designed based on the linear small-signal model of the impedance on the dc side and is simply tuned by a single low-pass filter parameter. The effectiveness of the proposed control method has been verified through simulation studies and experimental evaluations. A comparison of this proposed control methodology with typical PI controllers shows significant improvement in robustness during transient responses. It proves that IMC is one of the suitable candidates to resolve instabilities caused by non-minimum phase dynamics of three-phase Z-source inverters.