A method for actively controlling dynamic reaction forces in flexible structures subject to persistent excitations is presented. Since reaction forces are not directly measured in flexible structures, reaction forces are estimated by using the Kalman filter. The estimated reaction force is used as an error signal in the adaptive feedforward disturbance cancellation controller. In order to compensate the static effect of the truncated modes in the reaction forces, the residual flexibility matrix is used with the Kalman filter. The paper presents the formulation of the reaction forces in conjunction with the Kalman filter estimator and the adaptive feedforward controller. The results show that the dynamic reaction forces at its supports in a flexible beam test rir are well suppressed.