This paper investigates the detection of inter-turn phase faults in Permanent Magnet Synchronous Generators (PMSGs) using the Unscented Kalman Filter (UKF) compared to the Extended Kalman Filter (EKF). PMSGs are subject to several faults such as bearing, eccentricity, demagnetization, short circuit, and inter-turn faults. Accurate and early detection of the fault type is crucial for robust operation. Several techniques can detect these faults. UKF and EKF are presented here as one of the model-based fault diagnosis techniques. In the presented simulation, a comparison between the UKF and EKF estimation response of the fault has been shown. Both techniques have provided the ability to detect the inter-turn fault with the proposed PMSG fault model. However, the difference between the estimation response accuracy and speed plays an important role to decide the most effective technique.