FREE STATE - Deputy Justice and Constitutional Development Minister, Andries Nel, says the actions of a Bloemfontein art academy are "unacceptable".
The private Christian institution apparently offers to help "cure" homosexual students.
The SA Human Rights Commission has found the Creare Training Centre violated gay students' rights to equality, dignity and education.
The justice ministry had asked the commission to investigate claims of unfair discrimination at the training facility in January.
Minister Nel told the commission the centre had a prospectus "Relationship Etiquette", which includes a exclusionary provision opposing same sex relationships, and calling for discipline.
It also reportedly bans gay and lesbian students from attending lectures.
According to the centre's prospectus, it could "convert" gay students into heterosexuals through "rehabilitation", a Sunday newspaper reported in January.
Creare founder Cornelius van Heyningen has 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.
The commission recommended that the prospectus be reviewed and amended within three months.