Trump has given priority to Afrikaners, a white minority group he says is being persecuted. South Africa has objected to his characterisation.
Confederation of African Football president Patrice Motsepe has "zero tolerance" for corruption, which he says is "worse than cancer".
The foreign minister says the accusations, involving children, were investigated and found to be unsubstantiated.
The state department has also asked US citizens to "reconsider" travel plans to the West African country.
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