The Church of England made the explosive threat as the government proposes to introduce a legislation that allows civil marriage.

In a vociferous response to the government’s consultation on gay marriage, which closes on Thursday, the church says it cannot support the proposal to enable all couples, regardless of their gender, to have a civil marriage ceremony.

“Such a move would alter the intrinsic nature of marriage as the union of a man and a woman, as enshrined in human institutions throughout history,” it says.

“Marriage benefits society in many ways, not only by promoting mutuality and fidelity, but also by acknowledging an underlying biological complementarity which, for many, includes the possibility of procreation.”

 The submission warns of a potential clash between canon law – that marriage is between a man and a woman – and parliament, and puts prime minister David Cameron in a difficult position.

He has publicly endorsed gay marriage, but has still been criticised by other supporters of the proposals for allowing a free vote among Tory MPS.

The debate also comes at a delicate time for the Church of England, which is currently recruiting a new Archbishop of Canterbury, to replace Dr Rowan Williams.

Williams found it increasingly difficult to reconcile the wishes of the churches own factions, as well as those of a disparate worldwide Anglican communion of 80 million.

The church fears that even a legislation to limit same-sex couples to non-religious ceremonies, would be widened to religious ceremonies should a submitted at the European court of human rights.

This could make it impossible for the CofE to continue its role conducting marriages on behalf of the state, it warned.

Under the current law, anyone who is resident in England has a legal right to marry in his or her CofE parish church irrespective of religious affiliation. Around a quarter of weddings in England take place in CofE churches.

The debate is shaping up to be the biggest rupture between the state and the Church of England since it became the established church 500 years ago.

The church’s submission came under fire from gay rights campaigners such as Peter Tatchell, who accused it of “scaremongering, exaggerating the effects of same-sex marriage and advocating legal discrimination”.

He added: “The government’s proposals concern only civil marriages in register offices. They will have no impact on faith organisations or places of worship. Senior churchmen are protesting against a law change that will not affect them.

“They have no right to demand that gay couples should be banned from civil marriage ceremonies.”