One of the policy concerns in public sector labor relations is the dynamics involved in the representation and participation of the Board of Directors/Trustees (Boards) of state universities and colleges (SUCs) and government-owned and controlled corporations (GOCCs) as representatives of management in the negotiation process of the collective negotiation agreement (CNA). This unique relationship considerably influences the timely approval and registration of the CNA. This policy paper generally intends to determine best practices and bottlenecks in the negotiation, approval, and registration processes of CNAs among SUCs and GOCCs. The study adopts a mixed method case study design to gather quantitative data from reports of registration at the Civil Service Commission (CSC) and Bureau of Labor Relations and qualitative data through the conduct of key informant interviews among officers of public sector unions and human resource management officers or representatives from the management of the identified SUCs and GOCCs. The following are the key findings of this study: (1) some SUCs and GOCCs differ in terms of the extent of the representation and participation of the Board in the negotiation process and partnership/personal relationships between the management and members of the employees’ association influence the efficient processing of CNA; (2) most of the identified bottlenecks and best practices are born out of the type of relationship that is developed between the management and a union/employees’ association; (3) recommendations may be classified as either for policy intervention, for institutional process review, or for further research.