The same deficiencies make it harder to keep control of foreign aid programmes and ensure that they are being targeted wisely and effectively.
One reason why Uganda is being held up by Western countries as a model is its bold attempts to tackle these problems.
Its government is open about corruption. Earlier this year the finance minister admitted that, of the 75 per cent of government spending on goods and services, half is "swindled" from the system.
In the past the 10-11 donor governments had tried to by-pass the problem by dictating the terms of aid programmes and each sending regular inspection missions. But this took up so much of ministers' time it reduced their capacity to govern.
President Museveni's solution to corruption is bold: devolving power to regional districts. This prevents the capital's urban elite from amassing the country's scant resources for themselves. With so much money entering the education system - spending has tripled in five years - devolution is seen as crucial for keeping control of it close to where it is being spent.
Crucially, the president has built the trust of donor governments by ring-fencing a "poverty action fund", which can only be spent on water, education, health, rural roads, agricultural projects. and on monitoring of the spending. The fund is overseen by a board of stakeholders including non-governmental organisations, unions, churches, nd local government.
All donor governments have also agreed to sit down with the Ugandan government and thrash out a single national education programme between them. Now they are all trying to meet the same objectives.
An example of how devolution works is a project pioneered by Britain's Department for International Development to tackle the shortfall of 50,000 classrooms as the new pupils flooded into schools. Previously classroom construction had been centrally managed with materials distributed to the districts but the process was very slow and prone to corruption.
Two years ago the DFID funded a pilot project in four districts. The idea was to give responsibility directly to village schools. They were urged to apply for a construction grant. Once the neediest schools were identified by the district, the head was asked to pick a local contractor. Each project was managed by the parents and local community, who ensured the job was done properly.
In just a year, 416 classrooms were built, this way, compared to 300 in five years under the old system. The Ugandan government decided to adopt the methods nationally and has since built 9,000 classrooms in 12 months. With aid and debt relief funds, it will have built up to 37,000 by 2003.
Michael Ward, education adviser in Kampala for the DFID, said that, in his 15 years in development work, it is by far the most successful project he has been involved with.
He also points out that this method makes a significant economic impact on poor people's lives. "Because the contractor is local, the jobs go to local people," said Mr Ward."And the work is usually the biggest single capital investment the village has ever received."