Towards Regulation of App-Based Health Data in Africa

By Edrine Wanyama |

Digital health technologies are reshaping healthcare delivery across Africa. App-based systems now connect patients, clinicians, pharmacies, laboratories, and public health agencies, creating new opportunities to improve access, efficiency, and coordination of care. At the same time, they generate large volumes of highly sensitive health data, much of it moving across platforms, providers, and in some cases, national borders.

A new Policy brief by the Collaboration on International ICT Policy for East and Southern Africa (CIPESA) examines the critical need for robust governance of app-based health data in Africa.

The brief highlights significant health data governance gaps, which include the lack of health-specific AI regulation, fragmented legal, policy and institutional frameworks, and the unresolved distinction between wellness tracking and clinical care. These gaps fundamentally undermine health data handling and management standards, with flaws in consent, accountability, and cross-border data management requirements.

Across the continent, digital health applications now span multiple functions within health systems, from clinical management systems and electronic medical records (EMR) platforms to pharmaceutical logistics and supply chains. Alongside these systems, AI-enabled and specialist care platforms are expanding diagnostic and treatment capacity. Patient-facing applications are also expanding, particularly in chronic care, maternal health, and home-based services.

While these innovations are improving access to services and efficiency, they also introduce significant governance risks. Health data is among the most sensitive categories of personal data, capable of revealing medical history, reproductive health, mental health status, and genetic information. In app-based systems, this data is often processed by multiple actors, including developers, health providers, cloud infrastructure providers, and third-party analytics firms, many of which are not visible to users.

In practice, consent is often weak or poorly understood, data sharing arrangements are opaque, and users have limited visibility or control over the use of their information. This creates risks not only to privacy, but also to trust in digital health systems.

These risks are compounded by fragmented legal and institutional frameworks. Although many countries have enacted data protection laws and digital health policies, enforcement remains uneven and coordination between health ministries, data protection authorities, and digital regulators is often weak. This creates a persistent governance gap between the rapid expansion of app-based health systems and the capacity of institutions to regulate them effectively.

At the continental level, emerging frameworks such as the Africa Centres for Disease Control and Prevention (CDC) and global guidance such as the World Health Organization (WHO) Digital Health Strategy set important normative directions for secure, rights-respecting health data governance. However, translating these commitments into enforceable national systems remains limited, particularly in relation to interoperability, cross-border data flows, and platform accountability.

The brief calls for the adoption of a strategic governance architecture grounded in seven data governance principles, namely:

1. Data sovereignty that reflects African public health priorities, democratic oversight and defined accountability mechanisms;
2. Cross-border data flows where adequate and comparable safeguards exist and support reciprocal recognition arrangements among Data Protection Authorities (DPAs);
3. Consent, purpose limitation, and data minimisation that enable individuals to make informed decisions about participation and ensure secondary uses are subject to transparency and safeguards;
4. Interoperability and standardisation of systems to ensure integration and portability;
5. Governance of AI-based health tools that require algorithmic impact assessments, independent audits and ongoing monitoring;
6. Equity and inclusion to ensure systems do not further exclude vulnerable and marginalised communities; and
7. Accountability and institutional coordination through clear allocations of responsibilities across institutions, consistent oversight, enforcement, and compliance monitoring.

The principles are consistent with the CDC Health Data Governance Framework. Together with other continental instruments, they can support a harmonised, rights-respecting and secure health data governance in Africa.

The brief presents recommendations for various stakeholders which, if implemented, could foster a progressive and trustworthy digital health ecosystem in Africa. Among theses include:

For the African Union and Regional Bodies

• Support implementation of the Africa CDC Continental Health Data Governance Framework through clear timelines, monitoring mechanisms, knowledge sharing platforms, and technical assistance for member states.
• Develop a continental health-app certification framework, recognised across participating jurisdictions, covering consent requirements, interoperability standards, cybersecurity safeguards, data governance obligations, and algorithmic accountability.
• Facilitate regional data trust zones through reciprocal recognition agreements among Data Protection Authorities, enabling secure and accountable cross-border health data flows for disease surveillance, research collaboration, and pandemic preparedness.

For National Governments and Health Ministries

• Enact or strengthen health-specific data governance legislation that addresses the full data lifecycle in app-based health systems, including consent, purpose limitation, data minimisation, retention, breach notification, and cross-border transfers.
• Establish regulatory sandboxes to assess the safety, effectiveness, and governance implications of emerging digital health technologies before large-scale deployment.

For  Data Protection Authorities

• Conduct risk-based audits and impact assessments of high-impact health applications, including privacy, security, and algorithmic fairness, where AI systems are deployed.
• Develop sector-specific guidance on the processing of health, biometric, and demographic data, including standards for research use, secondary use, and commercial processing.
• Enter into reciprocal recognition arrangements with counterpart DPAs across Africa to support coordinated enforcement and trusted cross-border data flows.

For Health Service Providers

• Formalise data processing agreements with health app vendors and third-party processors, including provisions on security, breach notification, audit rights, and liability.
• Strengthen workforce capacity through regular training on health data governance, cybersecurity, incident reporting, and the responsible handling of sensitive health information.
• Implement strong authentication, access-control, and encryption measures to protect patient information throughout its lifecycle.

For App Developers and Platform Operators

• Embed privacy-by-design and security-by-design principles throughout the development, deployment, and operation of health applications.
• Provide clear and accessible consent mechanisms that enable users to understand and control how their health data is collected, shared, retained, and reused.
• Conduct regular testing and independent assessments of digital health tools to identify and address bias, accuracy concerns, and performance disparities across African populations.

For Health Service Consumers and App Users

• Exercise rights over personal health data, including rights of access, correction, portability, and deletion where provided under applicable legal frameworks.
• Use health applications that comply with relevant regulatory requirements and recognised data protection standards.
• Report suspected data breaches, misuse of personal information, or harmful automated decision-making outcomes to relevant regulators and oversight bodies.

Please read the full Policy Brief here.