Civilian–military collaboration in humanitarian crises has been encouraged globally; however, little is known about their diverse ethical viewpoints towards challenging and critical situations, which may cause difficulties in the partnership, and influence the outcomes of their mutual activities. The aim of this study was to identify the diversity of viewpoints and ethical decision-making during exceptional circumstances among civilian and military populations from two different countries, each with diverse background and healthcare organization structures. Possible scenarios, based on a systematic review of the literature, were introduced to Swedish and Polish civilian and military healthcare providers. Variations in the participants’ viewpoints and approaches to ethical decision-making were analyzed according to their characteristics, organizational belonging, and nationality. There were differences between both populations but also within the military and civilian groups, respectively. One significant factor influencing ethical viewpoints was participants’ nationality. Differences in ethical viewpoints between multiagency organizations should be considered in planning and implementation of future transdisciplinary and international collaboration in disaster and emergency management. Further studies and renewed educational initiatives are necessary to validate these differences and to navigate civilian–military as well as other multinational partnerships.