Equal Education and the Treatment Action Campaign say giving condoms to schools won't increase sexual activity but rather confront the gravity of sex.
"Providing condoms in schools would not amount to encouraging children to break the law," they said in a joint statement.
"It is arguable that the availability of condoms would help to confront young people with some of the gravity and consequences of sex and thereby amount to the opposite of encouragement."
EE and TAC called on the health and education departments to ensure the Integrated School Health Programme (ISHP), which included providing condoms to schools, went ahead. President Jacob Zuma announced the programme on October 9.
TAC and EE called on Basic Education Minister Angie Motshekga to clarify her position on the matter.
"Given that the health minister is willing to provide such condoms free of charge, it is arguable that minister Motshekga's refusal to provide said condoms is in breach of Section 134 of the Children's Act," TAC and EE said.
"Were that the case, she would be committing a statutory offence, for which she could be prosecuted. It is clear that the Children's Act makes this an offence because of the serious danger inherent in unprotected sex."
A recent call by Health Minister Aaron Motsoaledi for condoms to be distributed in schools, where parents consented, was welcomed by the National Association of People Living with HIV and Aids on Wednesday.
Secretary general Mluleki Zazini said in a statement that the HIV/Aids epidemic required a unique response, including the promotion of condom use and their distribution in schools.
This would reduce high rates of teenage pregnancy which often led to girls dropping out of school and of sexually transmitted diseases, Zazini said.
However, the African Christian Democratic Party and Inkatha Freedom Party raised concerns this would encourage underage sexual activity.
More than 500 health professionals would be trained to deliver the ISHP. Under the programme nurses would provide sexual health information and contraceptives, if the school governing body allowed this. – Sapa