Abstract This paper presents a novel control technique using Fuzzy Type-2 controller for regulating the frequency deviations in an independent Hybrid Power System (HPS). The HPS comprises of a wind system and a solar photovoltaic (PV) system as primary energy sources, along with Fuel Cells (FCs) as additional generation systems and Double Layer Capacitor (DLC) Banks as storage devices to meet the load demand. The frequency variations occur in the HPS due to the intermittency in power outputs from the primary sources, the load changes as well as any attacks in the system. The frequency regulation is achieved by effective coordination control of FC and DLC with the aid of a Fuzzy Type-2 controller and a high pass filter (HPF). The DLC technology adequately satisfies the residual power of hybrid systems resulting from the slow dynamics of FCs. The Fuzzy Type-2 controller is trained using an input-output data set of a PID controller whose gains are tuned to their optimal values using Monte-Carlo state estimators. The proposed system is simulated using real weather data to validate the capability of the Hybrid Power System (HPS) in supplying isolated loads while maintaining power frequency balance conditions. Also the HPS is subjected to attacks in daily load variation and the results are compared with the system without attacks. The simulation results show that the peak over shoots are reduced considerably but the settling time is 0.2 seconds in the system with no attacks where as the settling time is prolonged to 1.2 seconds with the attacks. This paper demonstrates the effectiveness of the Fuzzy Type-2 controller for the coordination control of DLC and FC to achieve generation-load balance condition in comparison with that of the PID controller for HPS system with and without attacks.