Background To ensure a high level of public health and environmental protection, authorities that deliver scientific expertise to inform decision-makers and the public at large need to be independent from external stakeholders and free of conflicts of interest. This independence requires effective rules for managing links of interest (LoIs) and a high level of transparency, including publication of declarations of interest (DoIs) where appropriate. In the particular case of plant protection products (PPPs) within the European Union, these requirements should apply to all Competent Authorities contributing to the marketing authorization processes. Methods A comparative analysis of LoIs management procedures was performed on a selection of ten National Competent Authorities from different member states (NCAs). This analysis was based on (i) the identification of 17 criteria aiming at characterizing good practices for LoIs management; (ii) a survey of ten NCAs, based on an analysis of their institutional websites and their responses to official mail requests. Results The comparative analysis showed: (i) a frequent lack of transparency of NCAs regarding their procedures for managing LoIs; (ii) a significant heterogeneity between the NCAs’ LoIs management rules, even though they are in charge of comparable missions regarding the marketing of PPPs; (iii) substantial gaps between the LoIs management procedures adopted by several NCAs and the good practices that are promoted by EFSA. Current limits on their practices regarding LoIs management might open ways for undue external influences on scientific expertise, and ultimately impact negatively the risk management options adopted by national or European authorities. Limitations of this study and its extension for a more thorough overview of the current LoIs management practices are also discussed. Conclusions LoIs management and transparency rules need to be improved across NCAs, given their contribution as (co-)rapporteurs or peer reviews participants to the health and environmental risk assessment steps of the EFSA processes. To this end, a common minimum set of rules should be defined by EFSA; recommendations are proposed, based on the best practices implemented by the investigated NCAs. Such progress would contribute promoting high-quality unbiased scientific expertise and enhance EU citizens’ trust.