Beyond to highlighting on the public institutions organizational structure and the challenges of reform implementation in Ghana public sector agencies in this paper, the researchers emphasized their analysis in the previous empirical investigation and scholar literature(s). Samiatu S. (2010),George a. (2006), The study revealed that Ghana public institutions while having an organizational structure, there are still some threats as potential challenges to reforms implementation such as: lack of professional competence and skill, weak management information system, incompatible human and institutional capability, and limited finance and budget. Public institutions organizational structure whether well designed or change internal rules are not enough to foster ownership and promote sustainable reform. To secure an effective reform implementation, the reformer shall setup mechanisms which promote public agency capacity building to improve public sector performance.