To enhance the security of industrial CAN networks in vehicles by transmitting covert information for the authentication of electronic control units. The research methods include a comparative analysis of existing approaches to constructing covert channels in vehicle CAN networks, as well as extended protocols used in CAN buses, to identify the most effective solutions for electronic control unit authentication. During the study, a covert channel scheme in the CAN FD network will be developed, and a test bench will be created to simulate its operation, taking into account various noise-based attacks. Additionally, the study will investigate the noise resistance of the proposed scheme and evaluate its applicability in real-world operating conditions. The results of the study demonstrate the successful development of a modified covert channel in the industrial CAN FD network of vehicles, resistant to noise. Based on a comparative analysis of existing protection and authentication methods in CAN networks, an optimal approach was selected, enabling the construction of a counter synchronization scheme for authentication, based on traffic optimization. The developed covert channel was integrated into a time synchronization system and tested on a bench, verifying its functionality under noise conditions. The testing results confirmed the high noise resistance of the proposed covert channel scheme, proving its effectiveness for use in automotive networks. Additionally, an analysis of the scheme’s applicability in real-world operating conditions was conducted, opening prospects for its implementation in actual vehicles using the CAN FD protocol. The scientific novelty of the work lies in the development and modification of a covert channel for authentication in the industrial CAN FD network of vehicles, resistant to noise. For the first time, a counter synchronization method for authentication based on traffic optimization is proposed, enhancing the security and reliability of the network. The study also includes a comparative analysis of the proposed scheme’s resistance to noise.