This paper studies the differences between the organisation of budget management in selected government administrations in the Western Balkans and the Republic of Moldova and good practice across the European Union (EU). It observes that the ministry of finance (MoF) in these administrations typically engages in direct budget negotiations with a large number of budget organisations. This practice is in stark contrast with the budgeting approach observed in the EU, where the MoF only deals directly with government ministries and a limited number of constitutional bodies. The paper highlights the adverse consequences for the strategic role of the MoF for fiscal policy, the accountability of line ministries for budgeting and service delivery in their sector and the introduction of modern public financial management instruments such as medium-term budgeting and performance-based budgeting. This paper recommends that governments reduce the number of first-level budget organisations and give line ministries more responsibility for budget management in their sector. At the same time, the paper recommends strengthening line ministries’ accountability for budget management towards the parliament.