For the reduction of unbalanced vibrations in a multi-input and multi-output flexible rotor system with electromagnetic actuators (EAs), conventional adaptive feedforward controllers (AFFCs) are very sensitive for changes in rotor spin frequencies. Although frequency updating is used in these controllers, a small variation in the rotor spin frequency can completely reduce their effectiveness. An adaptive notch filter is used in this research for the frequency estimation. By using this external frequency estimation, the performance of the conventional AFFCs can be enhanced. During changes in the rotor spin frequency, fundamental harmonics of the flexible rotor are also excited. Their amplitude is much higher compared to steady-state unbalanced vibrations, which can accelerate the wear and tear of components of EAs. By using feedback controllers, the amplitude of these fundamental harmonics can be reduced significantly. In real rotors with flexible bearing supports, any looseness of bolts and presence of transverse cracks can change system parameters significantly. Multiple harmonics are generated corresponding to even single spinning speed of the rotor. Robust stability as well as performance can be achieved in the presence of uncertainty and rotor crack nonlinearities using feedback controllers designed by mu-synthesis. By using the multiharmonic hybrid control, the higher harmonics can be compensated efficiently in case of a crack in rotor systems. The fast Fourier transform of the control signal can indicate the presence of a transverse crack in an online manner. In this way, active vibration control as well as rotor crack fault detection can be done simultaneously.