A Ugandan poster encouraging abstinence
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Ugandan President Yoweri Museveni has ordered the arrest and prosecution of former Health Minister Jim Muhwezi and his two deputy ministers at the time.
A report implicates them in mismanaging a grant from the Global Fund to Fight Aids, Tuberculosis and Malaria.
The fund suspended its grants to Uganda in 2005 after finding the health ministry seriously mismanaged money.
Mr Muhwezi was later dropped from the cabinet by the president. Several other employees face charges over the issue.
The report by the general inspector of government calls for all those implicated to pay back the money.
It alleges there was gross misuse of a $4.3m immunisation fund by the three.
The fund found there was a shortfall after money was exchanged.
Uganda has won praise for its vigorous campaign against HIV/Aids.
It has helped to reduce the prevalence of the virus - which reached 30% in the 1990s - to single-digit figures.
However, it has come in for recent criticism with some saying that under pressure from the US, it is now concentrating on abstinence, rather than all three parts of its Abstinence, Be faithful and Condoms (ABC) strategy.