In recent years there has been an increase in research conducted in the Middle East, with a corresponding increase in the challenges faced by members of the Research Ethics Committees (RECs). This study compares the structures of Omani and Jordanian RECs and investigates the perceptions of the challenges affecting the work of the REC members in Oman and Jordan. A convenience sample of 34 Omani and 66 Jordanian participants from 21 universities was recruited in this cross-sectional study. Almost 70% disagreed that the members of RECs are unqualified, providing comments without justification; half believed that members have limited experience in research, and almost three-quarters that they have different opinions regarding some ethical issues. No significant differences were found between Omani and Jordanian REC members regarding their perception of the challenges, except for the perception that reviewing proposals is a time-consuming task (p = 0.048) and that multi-REC centres are less available (p = 0.026). The regression model showed that there were significantly more male members of Jordanian RECs, and that Jordanian members were less likely to receive formal training. In conclusion, the current structure of RECs and the challenges faced by members need to be re-evaluated by decision makers to improve the overall quality of research activities, and to ensure that current REC members’ practices adhere to international standards.