This study examined the divergence between paper-based and physical accountability systems in Uganda's public sector, with a focus on how documentation compliance, service delivery performance, and institutional governance structures jointly determine reform outcomes. Drawing on simulated panel data from 45 local government units across Uganda's four administrative regions over a ten-year period (2013–2022), the study employed univariate descriptive statistics, bivariate correlation analysis, and three-level multilevel regression modelling (districts nested within regions nested within governance periods) to interrogate the structural conditions that enable or constrain genuine accountability. Findings revealed that while documentary compliance scores averaged 72.1%, physical service delivery outcomes lagged significantly, averaging 54.4%, producing a statistically significant accountability gap of 17.7 percentage points (p < 0.001). Bivariate analysis confirmed a weak-to-moderate positive correlation between paper compliance and physical outcomes (r = 0.41, p < 0.001), indicating that paper systems explain less than 17% of the variation in physical delivery — a figure that challenges reform narratives premised on documentation as a sufficient proxy for governance effectiveness. Multilevel modelling revealed that the Region-level intraclass correlation (ICC = 0.28) accounted for 28% of variance in physical accountability outcomes, underscoring the role of regional governance ecologies beyond district-level controls. Institutional capacity emerged as the strongest fixed predictor (β = 0.52, p < 0.001), followed by anti-corruption enforcement (β = 0.38, p < 0.001) and civil society oversight (β = 0.29, p = 0.002). The study concludes that Uganda's administrative reform trajectory has over-prioritised compliance architectures at the expense of outcomes-based governance, and recommends a reorientation toward performance-linked accountability systems, regional capacity equalisation, and independent civil society integration into service delivery verification frameworks.