Gay marriage threatens the establishment of the Church of England and could lead to it being forced out of its role of conducting weddings on behalf of the state, it has claimed.
The Church of England said introducing same-sex marriage would lead to an unprecedented clash between its own canon law - that marriage is between a man and a woman - and that of Parliament.
It also warned that in spite of ministerial assurances that churches would not have to conduct gay marriages, it would be "very doubtful" whether limiting same-sex couples to non-religious ceremonies would withstand a challenge at the European Court of Human Rights.
This could make it impossible for the Church of England to continue its role conducting marriages on behalf of the state, it warned.
The Church of England added that introducing gay marriage could also lead to challenges to civil partnership law, as removing the concept of gender from marriage while leaving it in place for civil partnerships would be unlikely to be "legally sustainable".
In a highly critical response to the Government's consultation on gay marriage which closes on Thursday, the Church of England said several "major elements" of the proposals had not been thought through properly and were not legally "sound".
The Rt Rev Tim Stevens, Bishop of Leicester, said the Church of England had been supportive of civil partnerships when the legislation was introduced eight years ago.
"We continue to be supportive of the gay community and want to see that inclusion in our society increased and developed," he said.
"I think the difficulty we have here is the substitution of equality for uniformity, that is to say that there can be no distinction at all between men and women."
He added: "The Government is seeking to meet what it perceives to be the needs of the gay community. I would say that the Church of England is sympathetic to those needs, we want to see a society in which gay people are fully included and their needs are fully provided for.
"But this does not amount to a basis for introducing a complete redefinition of the concept of marriage based on a consultation process which is at the very least rapid.
The Catholic Church in England and Wales joined the Church of England on Tuesday in attacking the government plans.
According to the BBC the Catholic Church encouraged people to sign a petition organised by the Coalition for Marriage. The petition, which had more than 500,000 signatures, was presented to Downing Street on Tuesday afternoon.
Under the current law, anyone who is resident in England has a legal right to marry in his or her Church of England parish church irrespective of religious affiliation and the minister of the parish is under a legal duty to conduct the marriage.
Around a quarter of weddings in England take place in Church of England churches with the number rising in 2010 by 4% to 54,700 compared to 52,730 in 2009.
The broadside from the Church of England will add to pressure on David Cameron, who has spoken out in support of gay marriage.
Cameron has come under fire from supporters of the proposals for allowing a free vote amongst Tory MPs to avoid a rebellion over the issue.
But other Tory critics have said they view the proposal as a Liberal Democrat policy distracting the Government from bigger challenges.
Former cabinet minister Liam Fox said on Sunday it was "a contentious issue but I have to say that I am much more in favour of social mobility than social engineering."
Ben Summerskill, chief executive of Stonewall, which campaigns for gay rights, said: "There's manifestly no evidence that the recognition of long-term same-sex relationships has any impact on the institution of marriage for heterosexuals.
"It seems odd that the Church of England should be obsessing about a few thousand gay couples once again when there are currently three million children in Britain living in single-parent households."
Human rights campaigner Peter Tatchell accused the Church of England of "scaremongering, exaggerating the effects of same-sex marriage and advocating legal discrimination", saying public opinion was overwhelmingly in favour of same-sex marriage.
Tatchell, co-ordinator of the Equal Love campaign to legalise same-sex civil marriages and opposite-sex civil partnerships, said: "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.
"It is absurd to suggest that allowing same-sex civil marriages would lead to legal challenges that could force churches to marry gay couples.
"Civil divorces are legal, yet there has never been a successful legal challenge to religious organisations that ban divorce. The courts recognise a distinction between civil and religious institutions."
A Home Office spokesman said: "The purpose of the equal civil marriage consultation is to enable us to listen to all views, including those of all religions.
"Marriage is one of the most important institutions we have. It binds us together, it brings stability, and it makes this country stronger. We have been 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."