Secure data exchange in the control system of unmanned aerial vehicles (UAVs) is an important aspect for preventing unauthorized access and safety of aerial vehicles. Given the problems of automatic dependent surveillance-broadcast (ADS-B) data protection, the safety level of UAV flight tasks and air traffic in general is significantly reduced. Therefore, the protection of ADS-B data is an urgent task. The object of the study is the process of steganographic protection of ADS-B format data. A relevant problem of estimating the probabilistic time characteristics of the steganographic protection process is solved, taking into account the features of data embedding in the ADS-B format container. To solve it, a mathematical formalization of the methods of finding probabilistic-temporal characteristics of steganographic systems was carried out. A model of steganographic data transformation operations based on the Chinese remainder theorem has been built. The main difference of the model is taking into account the features of the ADS-B format data. This made it possible to formalize and evaluate the time functions of steganographic encoding and decoding of UAV identifiers with an integrated ADS-B system. A model of steganographic data transformation operations based on the finite integral ring theorem has been constructed. A list of operations performed in the developed algorithm has been compiled. This made it possible to carry out mathematical formalization of operations for complex use in the model of steganographic protection of UAV identifiers with a built-in ADS-B system. The mathematical model was studied and the estimation of the random value of the time of steganographic transformation of data, as well as the confidence interval, was performed. With the help of the reported set of models, it is possible to estimate the probability of the algorithm’s execution time falling within the given interval. The results of the calculation of probabilistic-time characteristics could be used in models of a higher level of the hierarchy