Incorporating detailed 3D building data into national spatial data infrastructures (SDI) is associated with numerous technical and administrative challenges. This paper presents and discusses the challenges that have emerged within recent 3D mapping initiatives in Slovenia. The increasing availability and affordability of LiDAR and photogrammetric technologies have enabled the automated generation of comprehensive 3D building datasets. Despite these technological advancements, there are several difficulties in integrating these datasets with existing cadastral and topographic databases. Primary challenges include discrepancies in spatial accuracy, outdated building outlines, semantic inconsistencies, and varying classification methodologies among datasets. Moreover, maintaining these integrated datasets is complex due to differing update cycles across cadastral and topographic systems. Cadastral data requires rigorous administrative processes for updates, while 3D modelling of buildings typically relies on automated procedures. Additionally, the official status of cadastral data further complicates the integration. The challenges identified in the case of Slovenia can largely be generalized to systems in other countries, highlighting the necessity for strategic planning in data integration processes, considering both technical specifications and administrative frameworks, to use the full potential of 3D building data within national SDIs.