In this article the fibre reinforced polymer (FRP) composites shaft analysed as a Timoshenko beam. The prime objective of this research to reduce the vibration in composites shaft system. To utilize the active vibration control technique. Three different isotropic rigid disks are mounted on it and they also supported by two active magnetic bearing at its ends. The analysis work involves finite element, vibrational and rotor dynamic analysis of the system. Rotary inertia effect, gyroscopic effect kinetic energy and strain energy of the shaft are derived and studied. The governing equation is obtained by applying Hamilton’s principle using finite element method in which four degrees of freedom at each node is considered. Active control scheme is applied through magnetic bearings by using a controller containing low pass filter, notch filter, sensor and amplifier which controls the current and correspondingly control the stability of the whole rotor-shaft system. Campbell diagram, stability limit speed diagram and logarithmic decrement diagram are studied to establish the system stability. Effect of different types of stacking sequences are also studied and compared.