Uganda’s ambitious shift to programme-based national planning under the Third National Development Plan (NDP III) was meant to transform the way the government spends public money, delivers services, and measures results. Instead of ministries operating in silos, the country envisioned integrated programmes working together toward common national goals.
But after the expiry of the years in the period into NDP III implementation, a persistent mismatch between the traditional sector-based Public Financial Management (PFM) framework and the programme-based National Development Plan approach continues to undermine efficiency, accountability, and service delivery.
At the heart of the challenge lies a difficult reality: while Uganda has made major progress in digitising financial systems and improving oversight, implementation capacity remains weak, coordination fragmented, and corruption still drains public resources.
Bold shift in national planning
The NDP III marked a significant departure from Uganda’s previous planning model. The framework replaced fragmented sectoral planning with integrated, multi-sectoral programmes designed to improve coordination and strengthen public expenditure management.
Government also introduced modernised digital financial systems such as the Integrated Financial Management System (IFMS), Programme-Based Budgeting System (PBS), and Integrated Bank of Projects (IBP), all aimed at improving real-time tracking of public finances and projects.
According to Dr Wnnie Nabiddo, senior manager for research and development performance at the National Planning Authority (NPA), the reforms have yielded gains in budget transparency, accountability, and reporting.
‘The Public Financial Management framework has enhanced budget transparency and control by enabling more efficient, accurate, and real-time tracking of government finances and projects,’ she noted.
The Office of the Auditor General (OAG) also expanded its audit functions during the NDP III period, strengthening accountability through value-for-money audits and the now influential Certificate of Budget Compliance.
The certificate has become an important benchmark linking government expenditure to actual development results.
Capacity problem
Despite the reforms, Uganda’s transition to programme-based planning remains incomplete. Dr Nabiddo says many Ministries, Departments, Agencies (MDAs), and local governments still lack the technical and institutional capacity required to operationalise programme-based planning effectively.
In some institutions, she says fragmented planning practices still dominate. Planning remains aspirational rather than strategic, with weak prioritisation and poor sequencing of projects.
While digital systems are in place, which have improved reporting and expenditure tracking, implementation on the ground often tells a different story. Projects still face delays, cost overruns, and weak execution.
‘Closing implementation gaps requires streamlined processes, effective coordination, timely project execution, and enhanced capacity at all levels of government,’ Dr Nabiddo said.
Monitoring without action
Uganda has also strengthened monitoring and evaluation (M and E) systems during NDP III, introducing performance reporting frameworks and performance contracts for accounting officers. At the end of NDP Three, 30 percent of accounting officers’ performance assessments are tied to the implementation of NDP commitments.
Performance reporting has improved accountability, but experts say the findings are rarely used in decision-making.
‘There is limited follow-up and uptake of monitoring and evaluation findings,’ Dr Nabiddo observed. ‘M and E generates valuable insights, but follow-up and use remain inconsistent across MDAs and local governments.’
Weak implementation of recommendations has limited the impact of these systems on planning and budgeting.
The government has operationalised the Integrated NDP Monitoring and Evaluation System in some institutions, but full integration with key systems such as IFMS, PBS, Human Capital Management Systems, and other management information systems remains incomplete.
Many agencies still rely on stand-alone systems, manual reporting processes, and irregular reviews.
Data gaps undermining planning
Reliable statistics are essential for evidence-based planning, yet Uganda still struggles with fragmented and outdated data systems.
Although national statistics production has improved through surveys, censuses, and administrative data systems, gaps remain significant.
Data is often released outside the planning cycle, limiting its usefulness for budgeting and policy formulation.
Administrative systems across MDAs and local governments remain largely manual, fragmented, and unstandardised.
National evaluations also remain weakly institutionalised. According to experts, many evaluations are ad hoc, underfunded, and insufficiently integrated into the planning and budgeting cycle.
Oversight institutions have, nonetheless, become more assertive during the NDP III period.
The Office of the Auditor General expanded audit coverage across central government entities, statutory bodies, local governments, and development projects.
Meanwhile, Parliament has taken a more active role in scrutinising budgets, expenditure reports, and audit findings, contributing to stronger accountability debates.
Government has also made efforts to mainstream cross-cutting priorities such as climate change, disability inclusion, gender equality, youth empowerment, refugee management, science and innovation, health, nutrition, and implementation of the Sustainable Development Goals (SDGs), Agenda 2063, and East African Community Vision 2050. But integrating these issues consistently across all levels of government remains a challenge.
Corruption takes centre stage
As Uganda prepares for the Fourth National Development Plan (NDP IV), corruption has emerged as a central concern.
Dr Nabiddo revealed that during the recent Kyankwanzi retreat with Members of Parliament, President Yoweri Kaguta Museveni directed that corruption be incorporated as a key consideration within NDP IV and the country’s ten-fold growth strategy.
‘This directive echoes a clear recognition that corruption is a major structural impediment to growth,’ she explained.
Corruption, she said, undermines public expenditure effectiveness, weakens investor confidence, and constrains service delivery.
Government’s new reform push
The Acting Accountant General, Mr Godfrey Ssemugooma, says the government is pursuing reforms to tackle corruption, duplication of institutions, and financial mismanagement.
‘Public finance is the driving force that moves a nation from aspiration to achievement, from potential to prosperity,’ Mr Ssemugooma said.
According to him, Uganda’s macroeconomic stability depends not only on the Ministry of Finance and Bank of Uganda, but also on disciplined financial management practices across all government institutions.
‘When financial reports are timely, decision-making improves. When systems are credible, markets gain confidence in the government. When expenditure is well managed, deficits remain manageable,’ he said.
The reforms include tighter financial controls, automation of procurement and asset management systems, and restrictions preventing diversion of funds from capital projects to recurrent expenditure.
Government is also intensifying the Rationalisation of Government Agencies and Public Expenditure (RAPEX) programme, aimed at eliminating duplication and reducing bureaucracy.
Ssemugooma cited past arrangements where the Treasury allocated funds to one agency only for the money to be transferred again to another government institution.
‘This created unnecessary bureaucracy and duplication. RAPEX is about ensuring government works as one coordinated institution,’ he explained.
Domestic arrears and delayed projects
Despite progress, major financial management challenges remain unresolved.
Government is still struggling with procurement inefficiencies, delayed project implementation, domestic arrears, and constrained fiscal space.
For the first time in Uganda’s history, the government budgeted Shs1.4 trillion to clear domestic arrears. While payments were delayed pending verification by the Auditor General and KPMG, approximately Shs 900 billion has already been released.
Still, many government projects continue to miss deadlines, exceed budgets, or fail to meet expected quality standards.
Capacity gaps at both central and local government levels continue to affect service delivery. Mr Ssemugooma also acknowledged a deeper institutional problem: a culture focused more on compliance than outcomes.
‘So long as the law is followed, some institutions consider themselves successful whether they deliver results or not,’ he said. ‘That mindset shift-from compliance to measurable outcomes-remains a major challenge,’ Mr Ssemugooma said.
Private sector frustrations
The private sector says delayed government payments remain a major obstacle to economic growth.
Ms Erinah Masiga, head of finance at Uganda Baati Limited, said private firms supplying goods and services to the government still suffer from the delayed release of funds.
Delayed payments often affect cash flows, investment decisions, and business sustainability.