Numerous hospital laboratories in Indonesia need to implement improved bio-risk management (BRM) systems. There are many potential biohazards in laboratory activities that can impact health and the environment, leading to laboratory incidents. To minimize the impact and occurrence of such incidents, it is necessary to evaluate the implementation of BRM in every hospital laboratory that uses biological agents. This study was conducted in eight COVID-19 reference hospitals in Indonesia in the regions of Sumatra, Kalimantan, and Java, which have committed to implementing BRM systems in their laboratory activities. This research employed a descriptive study design and quantitative methods, with the aim of analyzing and evaluating the implementation of BRM systems in laboratories by assessing the achievements and gap analysis obtained from each laboratory. This research utilized primary data in the form of checklist forms referencing ISO 35001:2019 for the laboratory BRM system. Then, the assessments were based on virtual interviews conducted by the researcher with laboratory personnel as the primary data. The evaluation conducted on gap analysis from the seven clauses in ISO 35001:2019 across all hospitals revealed large gaps, particularly in three clauses: leadership, support, and performance. However, the aspects concerning organization, improvement, and performance evaluation were relatively satisfactory. Hence, there is a need for further improvement in leadership, support, and performance evaluation clauses. Additionally, it is essential to highlight the importance of comprehensive performance assessment, including proactive audits and continuous enhancements to achieve optimal bio-risk management.