The Free Presbyterian Church has come under pressure to further sever its political links with the DUP.
Mr Paisley intends to continue as a Free Presbyterian minister
Last Friday, after a five-hour meeting of the church's Presbytery, Ian Paisley announced he would step down as Free Presbyterian moderator in January.
The DUP leader also said he intended to continue his work as a clergyman.
However, the Concerned Free Presbyterians' website said it hoped to "completely disassociate" the church from the Stormont administration.
"A start has been made and it is our hope that Presbytery will now proceed to deal with the remaining issues," a statement on the website read.
It said these issues included "disassociating the church from the present Stormont administration completely".
Speaking to his congregation at Martyrs' Memorial Church in Belfast on Sunday, Mr Paisley said he had agreed to stand down because the church was facing a "very real crisis".
"While I am no longer going to carry the weight which I have carried for over 56 years as moderator of our Presbytery, I have news for you ... that I will be here and I am praying to God that I will be able to preach right to the end of my days," he said.
Mr Paisley has been elected moderator of the Free Presbyterian Church every year except one since he founded the church in 1951.
Professor Steven Bruce, who has written a book following Mr Paisley's church and political careers, said he believed the time was right for him to step down from the post.
"The church wants full-time ministers, it wants its clergy working for it and not somebody else," he said.
"I think a lot of people in the church will be generally happy with a gentle separation between the two of them.
"Both the party and the church have developed its own professional leadership.
"The idea of someone straddling the two becomes increasingly hard.
"Whatever the mechanics of this decision, I think everybody involved will be happy with it."