The Catholic Church has been vocal in its opposition to the creation of the body, saying that it will give the state control over religion.
President Edgar Lungu has appointed a Pentecostal pastor, Rev Godfridah Sumaili, as the head of the new ministry group.
Zambia Conference of Catholic Bishops (ZCCB) and the Council of Churches in Zambia (CCZ) said on their website that: "We neither see the creation of the said ministry as a top priority nor a prudent decision.
"After all, we believe that Zambians want their country to be a democracy rather than a theocracy."
Rev Dr Alfred Kalembo from the organisation added: "We believe that as churches and other faith communities, we have thus far been able to exercise our God-given mandate and meaningfully contribute towards national development without having such a ministry."
The groups said the Church and the State are both concerned about the common good and the well-being people and "as such, we see the need for the two to trust each other, engage in genuine dialogue and work as partners in promoting the development of its peoples, especially the poor."
It said the Church should not have to act as the state and politicians wish and should stand up for social justice exercising its "God-given mandate".
The President has spoken out, according to Vatican Radio, saying that Christians should not be intimidated by the creation of this special ministry group and that this would smooth out the relationship between the state and the Church.
President Edgar Lungu was re-elected in August, following a violent period of election campaigning.
The Church used this as an example of the importance of separation between church and state, saying it was "playing a vital role of being a voice of conscience calling a nation to order, especially in the aftermath of the 2016 general elections that have incurred on people scars of violence, division, tribalism and hatred."