Gauteng's Nazareth Baptist Church leader, Phakama Shembe, will be visiting hostels in Soweto from Sunday, where he will distribute condoms in an effort to combat Aids.
But the move has sparked controversy and has been criticised by church leaders in KwaZulu-Natal.
Mhlephila Mthethwa of the Buhleni faction of the church said the church did not condone his actions.
He said there were ways to teach men how to behave within the church, adding that going to hostels to distribute condoms was a disgrace.
"We don't even know this boy you are talking about," he said.
"In Gauteng we have priests whose duty it is to lead Shembe's subjects.
"This boy must stop doing things and claiming he represents the church," Mthethwa said.
He said Shembe was dragging the church's name into the mud.
Shembe said his visit was also in support of the 16 Days of Activism for No Violence Against Women and Children.
Patrick Dooms, Shembe's spokesman, said yesterday that condom distribution would not encourage people to engage in more sexual activity.
He said they wanted to hand out condoms because Aids is rife and it kills people every day.
"Inkosi ya maNazaretha will distribute condoms as part of his official acknowledgment that medical science should not be overshadowed by religious zeal," Dooms said.