The article presents a new modification of the the least squares Prony method. The so-called variable-frequency Prony method can be a useful tool for estimating parameters of sinusoidal components, which, in the analyzed signal, are characterized by time-dependent frequencies. The authors propose use of the presented method for testing the quality of electric energy. It allows observation of phenomena which, when using traditional methods, are averaged in the analysis window. The proposed modification of least squares Prony method is based on introduction and specific selection of a frequency matrix. This matrix represents frequencies of estimated components and their variability in time.