In the paper issues related to the design of a robust adaptive fuzzy estimator for a drive system with a flexible joint is presented. The proposed estimator ensures variable Kalman gain (based on the Mahalanobis distance) as well as the estimation of the system parameters (based on the fuzzy system). The obtained value of the time constant of the load machine is used to change the values in the system state matrix and to retune the parameters of the state controller. The proposed control structure (fuzzy Kalman filter and adaptive state controller) is investigated in simulation and experimental tests.