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Unmanned Aerial Vehicles (UAVs) are increasingly integrated into critical applications ranging from logistics and agriculture to defence and security operations, surveillance and emergency response. At the core of these systems lies the communication link between the UAV and its ground control station (GCS), which serves as the backbone for command, control and data exchange. However, communications links remain highly vulnerable to cyber-threats, including eavesdropping, signal falsification, radio frequency interference (RFI) and hijacking. These risks highlight the urgent need for secure communication protocols and effective defence mechanisms capable of protecting data confidentiality, integrity, availability and authentication. This study performs a comprehensive survey of secure UAV-GCS communication protocols and artificial intelligence (AI)-driven intrusion detection techniques.