The Evangelical Alliance Scotland, which represents two million Christians, said the proposals would result in less community involvement in policy-making.
A Private Member's Bill at the Scottish Parliament proposed by independent MSP John Finnie is seeking to take away voting rights from church representatives who sit on education committees.
Kieran Turner, a spokesman for the alliance, said: "There is nothing to gain from this proposal and an awful lot to lose.
"It is nothing but a wolf in sheep's clothing and is part of a wider agenda by small secularist groups to marginalise religion in public life.
"While on the surface this is about a secularist agenda to remove so-called religious privilege, in reality the consequence would be reduced community involvement in education policy."
Mr Finnie submitted his Private Member's Bill proposal last year seeking to abolish the mandatory involvement of religious representatives on local authorities' education committees.
Highlands and Islands MSP Mr Finnie, who quit the SNP last year after a row over Nato membership, said his bill would make local government more accountable and transparent to the electorate.
The move has been greeted with fierce opposition from churches, but has the support from secular groups.