It is known that some rotational machines such as compressors, pumps and so on often generate noises and vibrations due to periodic disturbances synchronised with the rotational speed. Vibration suppressing systems such as repetitive control are known to be effective to suppress the periodic disturbances. However, the control input of the repetitive controller may become larger and larger when the control input is saturated. This paper designs a generalised disturbance observer using the internal model principle that is effective to suppress periodic disturbances, and proposes a method that can make control performance deterioration minimal even if the control inputs are saturated. First, the proposed system estimates disturbances using the disturbance observer. Next, the estimated disturbances are passed into a filter of which the gain is one and phase lag is zero at the disturbance's frequencies, and are added into the control input in order to cancel the periodic disturbance. This filter is designed using the internal model principle, and the reason is explained why the filter should not be set to one. Some motor system simulations show that the phase lag of the estimated disturbances correspond to that of the periodic disturbances so that the method can make control performance deterioration minimal. The method is appropriate to rotational machine systems such as compressors and pumps in which the vibrations and noises should be avoided.