Enhancing public accountability in Indonesia's agricultural sector is critical to ensure effective management of government aid (subsidised fertilisers and quality seeds) and to support national food security. Transparency and resource optimisation issues persist in public administration, potentially disrupting the supply chain of essential plant production inputs. This study examines the determinants of accountability in agricultural program implementation by analysing the influence of the integrity system, internal control system (ICS) and transformative leadership. It also investigates the moderating effects of organisational commitment and environmental uncertainty on these relationships. Employing a quantitative survey design, primary data were collected from 210 government finance officials and staff involved in agricultural oversight. Structural equation modelling (SEM) was utilised to test the proposed hypotheses. The empirical results indicate that the integrity system (β = 0.168, p < 0.001) and transformative leadership (β = 0.142, p < 0.001) have a positive and significant influence on government accountability, whereas the internal control system does not demonstrate a direct significant effect (β = 0.082, p = 0.168). Crucially, the study finds that organisational commitment and environmental uncertainty act as significant moderators, strengthening the impact of integrity and leadership on accountability. These findings suggest that fostering a culture of integrity and adaptive leadership, supported by strong commitment, is more effective than relying solely on formal bureaucratic controls. This study offers practical insights for policymakers to formulate strategies that enhance governance in agricultural development, ultimately ensuring the timely delivery of inputs required for optimal crop yield and plant health.