As countries work to strengthen preparedness for future health emergencies, national public health agencies (NPHAs) are increasingly recognized as central to protecting populations and coordinating effective responses. Yet their structures, mandates and capacities differ widely. Understanding how these agencies are governed – and how governance affects their ability to prepare for and respond to crises – is critical for future health security.
To advance this agenda, the Alliance and the WHO Health Emergencies Programme have been undertaking a multicountry research initiative examining how governance arrangements shape the performance of NPHAs. The initiative brings together researchers and policy-makers from across regions to explore issues of autonomy, accountability, coordination and trust, and to generate practical insights about structure and reforms.
Workshop on country experiences at the World Health Summit
At the recent World Health Summit 2025 in Berlin, the Alliance and WHO Health Emergencies Programme organized a session highlighting country experiences on governance of national public health agencies: Strengthening national public health agencies for future pandemics.
The Rt Hon Helen Clark, former Prime Minister of New Zealand and Chair of the Alliance Board, noted that global instruments such as the Pandemic Agreement and the revised International Health Regulations will only succeed if national institutions are strong. She described NPHAs as “the institutional backbone of preparedness and resilience,” and emphasized that “a pandemic anywhere is a threat everywhere – preparedness begins at home.”
Dr Chikwe Ihekweazu, Executive Director of the WHO Health Emergencies Programme, reflected that the COVID-19 pandemic had tested every aspect of governance and leadership. “Agencies must be able to act quickly, cohesively and effectively when crises start,” he said. “Countries everywhere are now reforming or creating national public health agencies – in Africa, in Asia, in Europe – and we should not have to learn only through our own mistakes. By working together and sharing evidence, we can build the collective wisdom needed to guide how these agencies evolve.”
Speakers shared examples of reform from across contexts. Dr Johanna Hanefeld of the Robert Koch Institute highlighted how clear legal frameworks can protect scientific independence and credibility during crises. Dr S. Mahendra Arnold from Sri Lanka described efforts to consolidate several technical units into a national centre for disease control to strengthen coordination and communication. Dr Edson Rwagasore of the Rwanda Biomedical Centre noted that integrating programmes under one agency has improved efficiency and accountability. Professor Vernon Lee from Singapore’s Communicable Diseases Agency reflected that agencies must be “bulldogs, cats, diggers and builders – courageous, innovative, resilient and constructive.” In closing remarks, Dr Austin Demby, Minister of Health for the Government of Sierra Leone, cautioned that “as we build national public health agencies, there are some core functions – the research, the communications, the high-level thinking around it – but they should not be divorced from primary health care”.
Together, these experiences showed that while models vary, clarity of mandate, stable financing and the ability to speak with one trusted voice are essential foundations for preparedness and response.
Building a shared evidence base
Previously in September, the Alliance convened more than 40 representatives from ministries of health, national agencies, regional bodies and global partners for a three-day workshop in Addis Ababa, Ethiopia. The meeting provided a space to share early insights from 11 country case studies covering both established and newly created NPHAs, to learn from each other, and to reflect collectively on what constitutes effective governance in diverse institutional and political contexts.
Discussions highlighted that while NPHAs vary widely in their structures – from autonomous agencies to entities within ministries of health – they all operate at the interface between science, politics and society. The meeting reaffirmed that autonomy is not an end in itself but a means to ensure scientific independence, timely action and trust. Participants also began shaping manuscripts for a forthcoming journal series and identified priorities for continued peer learning through webinars, twinning initiatives and regional networks.
“Across countries, we see that governance challenges are remarkably similar,” said Lorena Guerrero Torres, Technical Officer at the Alliance. “By comparing experiences and documenting what works, we can move beyond tacit knowledge and build a stronger evidence base to guide NPHAs and countries in their reforms and establishment.”
From evidence to dialogue
The Alliance and the WHO Health Emergencies Programme also co-hosted a global webinar that expanded the conversation. Drawing on experiences from two research studies conducted in Pakistan and Japan, and insights from a review of 11 NPHAs, the session showed that governance arrangements of NPHAs differ widely and explored the interplay between autonomy, accountability and coordination between NPHAs and ministries of health.
Dr Miyako Otsuka from Japan and Professor Dr Babar Tasneem Shaikh from Pakistan presented key findings from their research studies, both studying major governance reforms in their countries. In the case of Pakistan, the study showed that despite the re-organization Act of the National Institute of Health (NIH) in 2021, its effectiveness is limited by unclear roles and fragmented coordination between federation and provinces, as well as insufficient resources and donor dependency. In the case of Japan, while the establishment of the Japan Institute of Health Security (JIHS), merging two national institutes, backed by legal reforms, has clarified roles and accountability, it has also created challenges such as culture integration and uneven implementation.
Participants agreed that strong coordination mechanisms, clear legal mandates and balanced autonomy and accountability enable NPHA to deliver their functions. However, it was also noted that governance cannot be reduced to organizational charts or legislation: it also depends on leadership, integrity and the capacity to navigate politics without losing sight of evidence and equity.
Building collective wisdom for future resilience
Together, the workshop in Addis Ababa, the global webinar and the World Health Summit session mark important milestones in building a community of practice on NPHA governance.
The work is highlighting how good governance is not only about institutional design, but also about the relationships, trust and accountability that sustain performance over time. As Dr Kumanan Rasanathan, Executive Director of the Alliance, observed in closing the World Health Summit session, “you cannot build trust in a crisis. These structures live or die according to the relationships built beforehand. Governance is always about power and relationships – and it will always be messy.”
The Alliance and WHO have been working with the network to highlight the importance of governance of these agencies, noting that it is often neglected. They will continue to convene this growing network through forthcoming publications and peer learning activities. By documenting how governance arrangements shape the effectiveness of NPHAs, the initiative aims to generate evidence, inform reform and strengthen countries’ capacities to safeguard health security for the years ahead.