The Very Revd Dr Norman Hamilton, Convener of the Presbyterian Church in Ireland's Council for Church in Society, said he was "troubled" by recent developments.
He said there was a direction of travel in which the "state is increasingly wishing to censor what the Church says and what Christians believe and practice".
"I hate saying that, but we are troubled by it," he added in an interview with Premier.
During the interview he cited the case of Ashers Bakery in Belfast which was found to have discriminated when it refused to make a cake promoting gay marriage.
He also spoke of the case of Pastor James McConnell who was found not guilty of grossly offensive remarks when he called Islam 'satanic' and 'heathen'.
"If the current direction of travel continues then there is clearly a problem of the state seeking to muzzle the faith based organisations right across the UK," he added.
He raised proposed new anti-extremism measures which would see anyone providing teaching to children for over six hours a week face Ofsted inspections. It's claimed this would include church weekends away, beach missions, summer camps, and church youth groups.
The clergyman added he was not pessimistic enough to suggest some churches with more traditional views may have to go 'underground'.
But he admitted he was worried by a "marginalisation of faith" within society.
