Abstract
BACKGROUND: National Public Health Institutes (NPHIs) are government-anchored, science-driven institutions that consolidate essential public health functions, including surveillance, laboratories, workforce development, and emergency preparedness. In Africa, NPHIs are central to the Africa Centers for Disease Control (CDC) New Public Health Order, yet progress remains uneven, with fewer than half of Member States having established functional institutes by 2023. Fragmented evidence on establishment pathways, governance models, and operational maturity limits comparative learning and policy guidance. METHODS: We conducted a scoping review following the Joanna Briggs Institute (JBI) methodology and reported in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) checklist. Peer-reviewed and grey literature published between 2010 and 2025 were systematically searched across PubMed (U.S. National Library of Medicine), Scopus, Web of Science, Embase, CINAHL (Cumulative Index to Nursing and Allied Health Literature), WHO repositories, Africa CDC publications, and International Association of National Public Health Institutes (IANPHI) reports. Eligible sources included case studies, institutional reports, policy analyses, and commentaries describing NPHI establishment, governance, functions, challenges, enablers, or outcomes. Data were charted and synthesised thematically into five domains: institutional establishment, governance and structure, resources and capacity, implementation factors, and outcomes and impact. RESULTS: Twenty-one studies were included, spanning country case studies (Nigeria, Liberia, DRC, South Sudan, Uganda, South Africa, Burkina Faso) and multi-country evaluations, continental surveys, and conceptual frameworks. Establishment pathways varied from Acts of Parliament and Presidential decrees to ministerial directives, and institutional models included autonomous/semi-autonomous, ministry-based, and networked/hybrid arrangements. Governance was consistently emphasised, with NPHIs positioned as science-based authorities coordinating surveillance, laboratories, and emergency response. Resources and capacity were shaped by donor support, Field Epidemiology Training Programs, and infrastructure investments, though underfunding and sustainability gaps persisted. Implementation enablers included political will, Africa CDC and IANPHI frameworks, and peer mentorship; challenges included fragmented functions, weak legal frameworks, and donor dependence. Reported outcomes included improved outbreak detection and response, expanded laboratory and surveillance systems, strengthened IHR core capacities, and enhanced institutional resilience. CONCLUSIONS: NPHIs are critical anchors of health security in Africa, but their development remains uneven. Legal frameworks, sustainable financing, and integration into continental networks are essential for maturation. This review provides the first consolidated evidence map of NPHI establishment and models in Africa, highlighting best practices, recurrent challenges, and priorities for future research and policy action. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12913-026-14473-7.