At present, an acoustic method of testing is used for inspection products of aviation equipment made of powdered structural materials. One of the main information parameters is the velocity of acoustic wave propagation. The reliability of the testing essentially depends on the accuracy of measuring the transmission time of the acoustic wave in the material, in other words, on the accuracy of measuring the phase shift between the emitted and reflected signal. To increase the accuracy of this parameter, it is proposed to use a discrete orthogonal method. The results of applying the proposed method for measuring the phase shift between two signals for different signal-to-noise ratios for different values of the phase shift are presented in the article. Comparison of the results obtained experimentally and by simulation is given. Simulation was performed in the Matlab system, where virtual signals were created with a given noise level. For experimental verification of the method, a two-channel generator was used, which made it possible to generate signals with the necessary phase shift and the signal-to-noise ratio. The paper proposes a scheme for measuring the phase shift of signals, which implements the discrete orthogonal method and has high noise immunity. The obtained data confirm the effectiveness of the proposed method, which makes it possible to provide an error in measuring the phase shift of harmonic signals of less than 1 ° with a signal-to-noise ratio equal to 10, and this accordingly provides an error in measuring the time interval of less than 1%. The article also describes the practical implementation of the proposed system for measuring the time interval between two radio pulses at a frequency of 5 MHz. As a testing object, a composite material of the LaB6-TiB2 type was used in the shape of a rectangular prism with a side dimension of 3 mm.