The Church of England has warned that proposals to legalise gay marriage could undermine its status.
It says giving civil ceremonies the status of marriage would "alter the intrinsic nature of marriage as the union of a man and a woman".
The Home Office said religious bodies would not have to conduct gay marriages but the Church also fears this could be challenged in European courts.
Gay rights campaigners accuse the Church of "scaremongering".
Civil partnerships were introduced in 2005 to give same-sex couples the same legal rights as married couples, but the law does not allow such unions to be referred to as marriages.
Responding to a consultation in England and Wales, the Church of England said government proposals to allow same-sex marriages by 2015 would "alter the intrinsic nature of marriage as the union of a man and a woman, as enshrined in human institutions throughout history".
It said marriage acknowledged "an underlying biological complementarity which, for many, includes the possibility of procreation".
The Church claims that plans to exempt religious organisations from performing gay marriages would be unlikely to survive legal challenges in domestic and European courts.
As such, the government's consultation exercise, which closes on Thursday, was "flawed, conceptually and legally", it added.
Tory MP Crispin Blunt conceded the government's aim "to protect, indeed proscribe, religious organisations from offering gay marriage" may be "problematic legally".
"But the proposal the government are putting forward is that marriage should be equal in the eyes of the state - whether it's between a same-sex couple or a man and a woman," he told BBC One's Breakfast.
But human rights lawyer Lucy Scott-Moncrieff, the vice-president of the Law Society, said the European court was unlikely to agree that any religious organisation would be forced to carry out same-sex marriages.
"But what it might say is that religious organisations should be allowed to if they want to," she told BBC Radio 4's Today programme, adding that "many" did.
The plans do not allow for religious organisations in favour of change to conduct gay marriages.
The Church says the role of Anglican clergy to perform marriages for any parishioner who wanted one might disappear, undermining the Church of England's role as the state church.
The Rt Rev Tim Stevens, Bishop of Leicester, said the Church was "trying to uphold a traditional of teachings and understandings about marriage" at a time when "many marriages are in difficulty".
"It's very unlikely that, in just a few weeks, a new, universally-acceptable definition of a fundamental social institution can emerge overnight like this," he told Today.
Ben Summerskill, chief executive of Stonewall, meanwhile, accused the Church of England of a "masterclass in melodramatic scaremongering that somehow this is the biggest upheaval since the sacking of monasteries".
He told Today there was "no evidence whatsoever that people will take legal cases against the Church of England" because "the opportunity to sue someone if they don't provide a wedding of your choosing" already existed in law.
"There are hundreds of thousands of people who get remarried everywhere and the churches already say we will not carry out such weddings.
"If there were lawyers and, indeed, excited claimants who wanted to take such a legal case, they would have already been taken in that context," he added.
Human rights campaigner Peter Tatchell, meanwhile, said the government's proposals only concerned civil marriages in registry offices and would have "no impact on faith organisations or places of worship".
The Home Office said it had made it clear that "no religious organisation will be forced to conduct same-sex marriages as a result of our proposals".
"We welcome the Church of England's response and we will be carefully considering all points of view before publishing the outcome of the consultation later in the year," a spokesman said.
In April, prominent Church of England figures wrote an open letter to the Times newspaper saying the Church had "nothing to fear" from the prospect of gay marriage.
The Catholic Church in England and Wales, meanwhile, has urged people to sign an online petition organised up by the Coalition for Marriage.
More than 550,000 people have so far signed the petition set up by the "umbrella group of individuals and organisations in the UK that support traditional marriage and oppose any plans to redefine it".