The effective implementation of policies at the ministry and national institution agency levels is vital for the functioning of the Chinese government. However, previous research has predominantly focused on policy implementation issues at the local-government levels. This study examines the execution dilemma faced by partially overstaffed units during the process of reforming the pension system of the public sector and national institutions from 2015 to 2022, with particular emphasis on how ministry and national institution agencies resolve policy conflicts during their creative implementation processes. The findings reveal that policy implementation at the ministry and national institution agency levels is characterized by a smaller gap in administrative status between the policy implementers and the recipients, a lower degree of information asymmetries, and smoother policy feedback channels. Consequently, when ministry and national institution agencies encounter execution dilemmas, the level of policy ambiguity tends to be lower and conflicts become evident earlier in the process. The nature of these conflicts evolves as the policy execution progresses. Unlike local governments, which often adopt various flexible implementation approaches, ministry and national institution agencies tend to resolve policy conflicts through prompt policy adjustments, facilitating collaborative interactions between the policy-making and the policy-executing bodies. This article offers preliminary insights into the conflict and adjustment patterns that differentiate ministry and national institution agencies from local governments in their creative implementation processes. Furthermore, it provides reference for the reform of the pension system in national institutions and the public sector.