The justice ministry has asked the Human Rights Commission to investigate claims of unfair discrimination at the Creare Training Centre in Bloemfontein.
"We trust the SA Human Rights Commission will be able to use its extensive powers to investigate this matter and to take the necessary and appropriate action," the ministry said in a statement on Friday.
"The notion that a person's sexual orientation can be changed at will, or by compulsion, feeds the very same homophobic attitudes that encourage the criminal and abhorrent practice of so-called corrective rape."
The Sunday Times reported this week that the Christian arts academy had come under fire for advertising that it could "cure" homosexual students.
According to the centre's prospectus they can "convert" gay students into heterosexuals through "rehabilitation", it reported.
Creare founder Cornelius can Heyningen denied the institution was discriminatory.
"We are catering for those who say 'I want to change as a homosexual'. That's not saying no homosexuals are allowed," he was quoted as saying.
He compared the academy's stance on homosexuality to a drug rehabilitation programme.