The linear algorithm for analysis of variable-frequency phase shift dependencies measured by the frequency-domain method is considered. The analysis is performed in terms of a multi-exponential model adapted for frequency domain. The algorithm is based on the linearization of the model with respect to the coefficients depending on the estimated parameters, and subsequent application of the linear weighted least squares method. The accuracy of the obtained parameter estimations depends on the way of determining the involved weighting factors. Comparative testing of the algorithm with several ways for calculating the weighting factors is done, the reasons affecting their quality were investigated. An approach for calculating weighting factors is proposed that increases the efficiency of the algorithm.