Objective The aim of this study was to verify the existence of conscientious objection to comprehensive health care for the victim of sexual violence, as well as to understand the service structure of institutions authorized in the health care system for victims of sexual violence in the state of Minas Gerais. Methods This is a quantitative, cross-sectional, descriptive, and analytical field study aiming to collect data from institutions authorized to assist victims of sexual violence in the state. The instrument was handed in to the coordinators of these services. Results It was found that 11% have no physician in service and that 31% had no training for this type of care. It was revealed that 85% of these institutions have already encountered patients wishing to have a legal abortion, but 83% of them have not had their request granted. There was a 60% presence of conscientious objection by the entire medical team, the main reason being religious (57%). Conclusion The assistance system is not prepared for comprehensive care for victims of sexual violence, especially in terms of legal abortions, with conscientious objection being the main obstacle. A functional referral and counter-referral system is needed to alleviate such a serious and evident problem. It is hoped that the research results will promote dialogues in the state that favor appropriate actions on legal abortion, and respect the medical professional, in case of conscientious objection.