The increased dependence on IT and rise of security threats in organisations has led to the awareness of the need for adopting formal IT governance practices. However, how far have organisation came to realise the implementation of these practices is yet unknown at least in the Malaysian context. The article discusses information technology governance practices in public sector agencies from the perspective of an emerging country like Malaysia. The study sets forth to explore how the Malaysian public sector agencies implement IT governance through structure, process and relational mechanisms. This research uses qualitative approach in selected public sector agencies in EPU, ICU, MoF and CGICT. The result shows that each public sector agency define IT governance structure, process and relational mechanisms to align IT and business, thus enabling collaboration between business units and IT. Each public sector agencies in this case study practices IT governance structure, process and relational mechanism to align IT and business using different approaches based on organisational context.