Accelerating work on genome editing is regenerating biotechnology-related innovations in the agricultural and food sector. It challenges the institutional capacity of developing countries to regulate these risks. From a methodological point of view, we characterize the risk assessment system of Genetically Edited Plants (GEPs) in Madagascar through expert opinion surveys and by analysis of the main legislative and regulatory texts. The results show a dichotomy between a poorly functioning legal biosafety system and a potentially mobilizable inter-organizational scientific network. Collaborative mechanisms with civil society and the scientific community in risk assessment are difficult to make effective due to the weaknesses of the existing methodological and regulatory framework. The involvement of socio-economic actors in risk assessment processes and institutional capacity building are targeted as necessities to regulate risks linked to GEPs in developing countries.