Extended Kalman Filter (EKF) and Unscented Kalman Filter (UKF) based controllers for a class of hybrid systems, namely autonomous hybrid system (AHS), are proposed in this work. The stability in the performance of EKF and UKF based controllers were analyzed using experimental setup of hybrid three-tank system under variety of real-time uncertainties and operating conditions such as servo-regulatory operations, process-model parameter mismatch, initial condition variations and some hand valve faults. Quantitative comparison of the performance was made in terms of integral square error criterion and control signal generation time. The result confirms the efficacies and robustness of the controllers under the considered operating conditions.