Integral resonant control (IRC) is an effective vibration control technique for flexible structures including multiple vibration modes, even though the controller is a simple first-order system. However, IRC can not be directly applied to flexible structures with rigid body modes. This paper proposes a new method to apply IRC by choosing an angle difference output in which the rigid body modes are unobservable but only elastic modes observable. The proposed method is effective for applying IRC to torsional vibration systems where the control objective is to reduce only torsional vibration modes while leaving the rigid body mode preserved. However, side effects such as an inverse response and a brake effect occur depending on the choice of the controller parameter. This paper clarifies the condition for the inverse response and the magnitude of the brake effect on the rigid body motion analytically. A new design method for the IRC controller is then presented based on the trade-off between the brake effect and the vibration suppression performance.