The article is focused on research of an attack on the quantum key distribution system and proposes a countermeasure method. Particularly noteworthy is that this is not a classic attack on a quantum protocol. We describe an attack on the process of calibration. Results of the research show that quantum key distribution systems have vulnerabilities not only in the protocols, but also in other vital system components. The described type of attack does not affect the cryptographic strength of the received keys and does not point to the vulnerability of the quantum key distribution protocol. We also propose a method for autocompensating optical communication system development, which protects synchronization from unauthorized access. The proposed method is based on the use of sync pulses attenuated to a photon level in the process of detecting a time interval with a signal. The paper presents the results of experimental studies that show the discrepancies between the theoretical and real parameters of the system. The obtained data allow the length of the quantum channel to be calculated with high accuracy.
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