The problem of aircraft collision with birds (bird strike) is becoming more relevant with the growing trends of air transportation. According to the International Civil Aviation Organization (ICAO), over the seven-year period, 97751 aircraft collisions with animals in 105 countries around the world were recorded. In approximately half of the cases (56093 incidents), damage to the aircraft of various types is reported. According to some estimates, the annual damage from aircraft bird strikes is about 610 million US dollars. The article analyzes the effect of the aircraft bird strike threat (ornithological danger) on flight safety. The statistics of the aviation incidents with birds for the period 2010–2022 according to the figures from ICAO and the Federal Air Transport Agency of Russia are considered. The problems of risk assessment and ornithological flight safety and existing research works in this scientific field are analyzed. The main problems and shortcomings of the existing approaches are emphasized and discussed. A new concept for ornithological flight safety by dividing threats into those in a field of partial uncertainty and those in a field of deep uncertainty is proposed by the author. Making decisions in a particular field requires the use of specific tools. To solve the problem of ornithological flight safety under the threats in a field of deep uncertainty, a Dynamic Adaptive Planning (DAP) tool, that allows to develop and maintain the work of the plans with constant monitoring of the quality of their implementation is proposed. An example of the functioning of a decision-making algorithm and the assignment of critical points (triggers) to monitor the effectiveness of an airline’s plan with the aim of achieving specified ornithological flight safety indicators is given. An analysis of the results of the work showed that solving the problems in a field of deep uncertainty is a complex scientific task, however, the use of the new tools for scenario modeling will improve the quality of the Airline operation in providing ornithological flight safety, which will ultimately have a positive effect on reducing the risk of aviation incidents.