The National Indigenous Knowledge Registration System (NIKRS) initiative is developed in phases with the first phase focusing on African Traditional Medicine (ATM) and Traditional Food for implementation because these two themes are most at risk in terms of Intellectual Property exploitation and bio-piracy. Mitigating this risk required careful design of the system, particularly in terms of security and the management of the data. Care was taken to design the National IKS Management System (NIKMAS) such that it will support, on a national scale, the recordal, management and protection of Indigenous Knowledge (IK) with potential benefits, especially in the absence of relevant legislation (i.e. Sui Generis on IKS). The importance of securing confidential and secret information against unauthorised exploitation was also a major design consideration. In support of the National Recordal System, NIKMAS comprises a semantic digital repository with custom-developed metadata, schemata and a sophisticated security model to protect and preserve Indigenous Knowledge (IK), an advanced semantic search engine, a cataloguing and an overarching integration system, architecture that combines the subsystems into a coherent, fit-for-purpose system. NIKMAS, as the information technology management engine of the IK Registration is connected to IKS Documentation Centres and have been developed as an implementing platform to support communities to record and update information about their knowledge at the IKS Documentation Centres (IKSDC). One of the main drivers of the IK policy relates to the development of services provided by Indigenous Knowledge holders (IK holders) and practitioners, with a particular focus on IK with a scientific base. In order to support this driver, NIKMAS strives to provide technology support to IK holders and practitioners that will allow them to protect their IK and to benefit from value-bearing services and products that are created using their IK. NIKMAS will therefore provide a single access point to IK captured at distributed points in the NIKRS initiative and will contain links to other resources and databases containing relevant IK information managed in various institutions or government departments.