Abstract Background While patient safety incident reporting is of key importance for patient safety in primary care, the reporting rate by healthcare professionals remains low. This study aimed to assess the effectiveness of a risk management program in increasing the reporting rate within multiprofessional primary care facilities. Methods A nation-wide cluster-randomised controlled trial was performed in France, with each cluster defined as a primary care facility. The intervention included professional e-learning training, identification of a risk management advisor, and multidisciplinary meetings to address incident analysis. In the first observational period, a patient safety incident reporting system for professionals was implemented in all facilities. Then, facilities were randomised, and the program was implemented. Incidents were reported over the 15-month study period. Quasi-Poisson models were used to compare reporting rates. Results Thirty-five facilities (intervention, n = 17; control, n = 18) were included, with 169 and 232 healthcare professionals, respectively, involved. Overall, 7 out of 17 facilities carried out the entire program (41.2%), while 6 did not hold meetings (35.3%); 48.5% of professionals logged on to the e-learning website. The relative rate of incidents reported was 2.7 (95% CI = [0.84–11.0]; p = 0.12). However, a statistically significant decrease in the incident rate between the pre-intervention and post-intervention periods was observed for the control arm (HR = 0.2; 95% CI = [0.05–0.54]; p = 0.02), but not for the intervention arm (HR = 0.54; 95% CI = [0.2–1.54]; p = 0.23). Conclusion This program didn’t lead to a significant improvement in the patient safety incident reporting rate by professionals but seemed to sustain reporting over time. Considering that the program was fully implemented in only 41% of facilities, this highlights the difficulty of implementing such multidisciplinary programs in primary care despite its adaptation to the setting. A better understanding of how risk management is currently organized in these multiprofessional facilities is of key importance to improve patient safety in primary care. Trial registrations The study has been registered at clinicaltrials.gov (NCT02403388) on 30 March 2015.