Distributed energy resources (DERs) such as wind turbines and solar panels have fluctuating power generation profile. Also, uncertainty of DERs & loads can bring about complexity in functioning of protection for Microgrids (MGs). Thus, the operation of classical protection methods used in distribution networks may fail for MGs. In this context, this study presents a new protection methodology for discriminating between uncertain and asymmetrical / symmetrical events in MG. A detection method using covariance analysis of wavelet transform (CAWT) and a classification method based on fuzzy logic controller (FLC) using this analysis are presented. The proposed methods are evaluated under various conditions, including fault resistance, fault inception angle, and fault location. Furthermore, variation of solar irradiance levels and source strength has been taken into consideration to validate the performance of the proposed protection methodology. An advantage of the proposed methodology is that the relationship among phases using a covariance analysis proves the presence of the fault. Another advantage is that the discrimination between uncertain and ASF&SF events was discussed, and the faulted phase(s) was/were accurately identified through FLC. Besides, the efficiency of introduced CAWT&FLC-based methods was confirmed on MG configurations such as radial and mesh. In addition, the presented protection methodology became more efficient when combined with the detection of uncertain events.