The Global Fund to Fight Aids, Tuberculosis and Malaria has suspended its grants to Uganda because of "serious mismanagement" of funds.
Girls are being encouraged to practise abstinence
An investigation carried out for the Global Fund said it found a shortfall when grants in dollars were converted into Ugandan shillings.
A Ugandan spokesman said the decision was not "fully informed".
Uganda is often held up as a model of how to fight HIV/Aids, with infection rates falling from 15 to 5%.
A spokesman for the Global Fund said it still wanted to continue working with Uganda's National Aids Commission directly, so the provision of condoms and anti-retroviral drugs would not be interrupted.
Uganda has received some $45m out of $201m it had been allocated in a two-year programme.
The problems allegedly centred on the Project Management Unit (PMU) at the health ministry, the Global Fund said.
"The Global Fund is gravely concerned that this mismanagement has reduced the effectiveness of the programme," the fund wrote in a letter to the Ugandan finance ministry, seen by London's Financial Times newspaper.
Uganda's health minister would be holding talks with the Global Fund about the suspension, a government spokesman said.
The fund said five grants would be suspended until the end of October and that any resumption would depend on the PMU being dismantled.
Uganda's anti-Aids campaign has recently been criticised, with some saying that under pressure from the US, it is concentrating on abstinence, rather than all three parts of its Abstinence, Be faithful and Condoms strategy, ABC.