The paper analyses how knowledge systems and epistemic cultures contribute to development planning through conduct of a microqualitative sociological case study of the health sector in Indonesia. The data were attained from 37 in-depth interviews and a stakeholder engagement workshop conducted in Gunungkidul, Yogyakarta, complemented with documentary media analysis. Our findings show that centralisation continues to exist in the development planning practice within the decentralisation era. This is shown through dependence on budget prescriptions and indicators from the centre in Jakarta. Further, this study demonstrates how the integration of indicators in the development planning process is hampered by myopic practices of government officials at the district level where there is evidence of an absence of verified knowledge in the Health Bureau of the District of Gunungkidul. Furthermore, there is dependence on data and information from volunteers in the Health Integrated Service Post (Posyandu) at the local village level. This study reveals, therefore, that development planning operates at three levels, yet with different knowledge systems and epistemic cultures at each level: central, district, and village.