The problem of cross-professional interaction between the pilot and air traffic controller (ATCO) is crucial to ensuring air traffic safety. In maintaining flight safety, it is important to organize high-quality collaborative decision-making (CDM) between the flight crew, ATCO, and other stakeholders based on their operational reliable communication in real-time. Therefore, the elaboration of CDM models for optimization of cross-professional interaction “pilot-ATCO” during their collaborative practical training is an actual problem. Based on the situation-based approach the structure of collaborative practical training of the pilots and ATCOs in a common educational environment is defined. The scheme of CDM by aviation specialists in an emergency to provide timely, competent, and reasonable recommendations of ATCO and other operators to the pilot under various disturbing actions is developed. The individual and CDM matrices for the different aviation specialists in the case of aircraft collision with a bird during takeoff are built. The optimal alternative for flight completion follows the operators’ individual and collaborative decisions based on the Wald, Laplace, and Hurwitz criteria is determined. The consistency between the pilot and ATCO estimates of the objective factors in the emergency “Collision with a bird during takeoff” based on Spearman’s coefficient is verified. Designed in the future based on big data analysis/machine learning tools an Intelligent System of Collaborative Decision-Making during the Training (IS CDM-T) for the collective practical training of the aviation specialists will allow for enlarging the efficiency of the air navigation system operators’ cross-professional interaction in emergencies.