This research investigates the challenges and factors that influence the implementation of research data management (RDM) in Indonesian research institutes. This study conducted in-depth interviews with six data managers from five Indonesian research institutions using a qualitative research approach. The interview data were analyzed using NVivo software, and the TOPE framework guided the identification of factors and challenges in (RDM) implementation. Critical aspects in RDM implementation are applications, hardware, culture, organizational units, institutional policies, leadership support, awareness, knowledge, education, skills, funder regulations, and government policies. Challenges in RDM implementation encompass access control, data quality, ease of use, building trust, availability of responsible staff, user understanding, researchers’ resistance, awareness, and inter-institutional relations. Research on data management, especially in developing countries like Indonesia, is limited. This study contributes by providing a high-level overview of research institutions in Indonesia, enhancing their understanding of the challenges and critical aspects involved in establishing effective RDM within their institutions. © The Author(s) 2024