This paper presents an advanced framework for securing 6G communication by integrating deep learning and physical layer security (PLS). The proposed model incorporates multi-stage detection mechanisms to enhance security against various attacks on the 6G air interface. Deep neural networks and a hybrid model are employed for sequential learning to improve classification accuracy and handle complex data patterns. Additionally, spoofing, jamming, and eavesdropping attacks are simulated to refine detection mechanisms. An anomaly detection system is developed to identify unusual signal patterns indicating potential attacks. The results demonstrate that machine learning (ML) and hybrid models outperform conventional approaches, showing improvements of up to 85% in bit error rate (BER) and 24% in accuracy, especially under attack conditions. This research contributes to the advancement of secure 6G communication systems, offering details on effective defence mechanisms against physical layer attacks.