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Abstract Background During the Covid-19 pandemic, family medicine practices (FMPs) changed to improve safety against new coronavirus infections for both patients and employees. Protocols for treating patients with suspected Sars-Cov-2 infections were established to protect medical staff and other patients from being infected. However, these protocols also led to increased safety risks, such as delays in treating patients with other medical conditions. This exploratory study aimed to investigate safety risks in treating patients in FMPs during the Covid-19 pandemic and to suggest improvements to prevent Covid-19 in FMPs in Slovenia. Methods A cross-sectional study was rolled out in FMPs in Slovenia as part of the international Pricov-19 study. Data collection on safety management during the Covid-19 pandemic in FMPs in Slovenia took place from November 2020 until January 2021 using a self-administered online survey for FP working in Slovenia. A chi-square test, ANOVA, independent samples t-test or bivariate correlation test was performed to explore associations regarding the safety of patients’ management variables. Results From the 191 participating family physicians (FPs) (15.2% response rate), 54.8% reported having treated patients with fever (not Covid-19) late due to the new protocols at least once, and 54.8% reported patients with urgent conditions having been seen late at least once due to not coming. In the suburbs and rural environments FPs more often reported that at least once patient with a fever (not Covid-19) was seen late due to the protocol (p = 0.017) and more often reported that at least once patient with an urgent condition was seen late due to not coming to their FP (p = 0.017). The larger the practice, the more they reported that at least once a patient with fever (not Covid-19) was seen late due to the protocol (p = 0.012) and the more they reported at least once a patient with an urgent condition was seen late due to not coming to their FP (p = 0.012). Conclusion Covid-19 affected the safety of patient management in FMP in Slovenia. The most common problem was foregone care. Therefor, protocols for chronic patient management in the event of epidemics need to be established.