The SA Council of Churches was neither informed of nor invited to the recent formation of the National Interfaith Leaders Council (NILC), it said on Wednesday.
"Although we do not presume that our exclusion was malicious, but the SACC is disappointed at not having been offered the courtesy of invitation," the council said in a statement.
The group said it had problems with the founding document of the NILC.
It has made contact with the office of the president, the NILC's leaders and the ANC's commission for religious affairs to find an "amicable way forward".
The council would host a meeting of church leaders soon to discuss the matter.
"e urge all SACC members to either put on hold or consider carefully the implications of their participation in the NILC, until the SACC has clarified a number of issues with the NILC leadership."
The SACC encouraged unity and mutual respect among religious bodies in the country, it said. "We also remain committed to collaborating with various faith traditions and government in combating poverty, moral degeneration, crime and social disintegration."
The NILC was formed last month and chaired by Rhema pastor Ray McCauley.
According to the government, the NILC is a mass-based group of religious leaders from across the country which reflects all the major faiths practised in South Africa.
The NILC could not immediately be reached for comment. - Sapa