Responding to a consultation on the issue in England and Wales, the Church said the legislation was "shallow".
Government plans to open marriage to gay couples by 2015 could undermine its status as the state church, it said.
The Home Office said religious bodies would not have to conduct gay marriages and that it was considering all views.
The plans do not allow for religious organizations in favors of change to conduct gay marriages.
Gay right campaigners accused the Church of "scaremongering".
The Church of England said by opening marriage to gay couples, an institution defined for centuries to be exclusively between a man and a woman would have its meaning "hollowed out" and reduced to the level of a "content free", "consumerist", agreement.
Church officials claimed the exemptions from performing gay marriages, which the proposals suggest for religious organizations, would be unlikely to survive legal challenges in domestic and European courts.
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-intercourse 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 "very tender to religious sensibilities".
If the issue was taken to the European court, judges were unlikely to agree any religious organization would be forced to carry out same-intercourse marriages, she told BBC Radio 4's Today programme.
"But what it might say is that religious organizations should be allowed to if they want to," she added.
"What we do know is there are many religious organizations that do want to be able to carry out same-intercourse marriages."
The Church insists the age-old idea of marriage as being for procreation, and needing to be consummated, would not apply to same-intercourse marriage
It says the duty 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.
And it warns creating "religious" and "civil" marriages with differing understandings of their purpose and character would serve to weaken and dilute the institution for everyone.
The Rt Rev Tim Stevens, Bishop of Leicester, said the Church had supported civil partnerships when the legislation was introduced eight years ago and continued to be supportive of the gay community.
"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 said.
"From a standing start within three months to arrive at a fully considered, weighed and articulated redefinition of a fundamental social institution which has been thought about in one particular way for centuries... to change all that on the basis of a consultation like this seems to be at the very least unwise and ill considered."
BBC