"While it is not morally prudent to preach the use of condoms as if they are the saviour from the pandemic, we should not fall victim to the conservative dogma that condoms are inferior," SACC general secretary Molefe Tsele said in a statement on Wednesday.
He said science had shown that, when used correctly and consistently, condoms could prevent the transmission of diseases.
Tsele's comments come two days after religious leaders met with Health Minister Manto Tshabalala-Msimang at a Religious Leaders' Forum in Johannesburg.
There, they criticised the government's promotion of condoms to prevent the spread of HIV/Aids and other infections advocating instead for faithfulness and abstinence.
Tsele said although it was entirely appropriate for religious leaders to "express their moral and strategic concerns" as part of the national debate on HIV and Aids they "should not pretend that their ethical misgivings are validated by scientific evidence."
During the 2001 national conference, the SACC adopted a resolution which Tsele said called on churches to "encourage the use of measures necessary to prevent infection".
This is in addition to promoting sexual abstinence and faithfulness in marriage.
He said all of SACC's 26 member denominations have reaffirmed that resolution.
"Condoms remain an essential pillar of the 'ABC' (Abstain, Be faithful, Condomise) approach. This was the formula that proved successful in Uganda, despite Washington's recent efforts to downplay the role of condoms," said Tsele.
He said churches should recognise that the government's HIV/Aids prevention strategy was based on the best scientific and medical data available.
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