To identify high-priority risks in a clinical trial investigating the use of radiation to alleviate COVID-19 pneumonia using a multi-phase failure modes and effects analysis (FMEA). A comprehensive FMEA survey of 133 possible causes of failure was developed for the clinical trial workflow (Phase I). The occurrence, severity, and detection risk of each possible cause of failure was scored by three medical physicists. High-risk potential failure modes were identified using the risk priority number (RPN) and severity scores, which were re-scored by 13 participants in radiation oncology (Phase II). Phase II survey scores were evaluated to identify steps requiring possible intervention and examine risk perception patterns. The Phase II participants provided consensus scores as a group. Thirty high-priority failure modes were selected for the Phase II survey. Strong internal consistency was shown in both surveys using Cronbach's alpha (αc≥0.85). The 10 failures with the largest median RPN values concerned SARS-CoV-2 transmission (N=6), wrong treatment (N=3), and patient injury (N=1). The median RPN was larger for COVID-related failures than other failure types, primarily due to the perceived difficulty of failure detection. Group re-scoring retained 8/10 of the highest-priority risk steps that were identified in the Phase II process, and discussion revealed interpretation differences of process steps and risk evaluation. Participants who were directly involved with the trial working group had stronger agreement on severity scores than those who were not. The high ranking of failures concerning SARS-CoV-2 transmission suggest that these steps may require additional quality management intervention when treating critically ill COVID-19+ patients. The results also suggest that a multi-phase FMEA survey led by a facilitator may be a useful tool for assessing risks in radiation oncology procedures, supporting future efforts to adapt FMEA to clinical procedures.