It expressed its support for civil partnerships but said that opening marriage up to same-sex couples "would confer few if any new legal rights" on their union.
"The issue of whether marriage should be redefined to include those of the same-sex is a more complicated picture than has been painted," the Church said.
"Arguments that suggest 'religious marriage' is separate and different from 'civil marriage', and will not be affected by the proposed redefinition, misunderstand the legal nature of marriage in this country.
"They mistake the form of the ceremony for the institution itself.
"Currently, the legal institution of marriage into which people enter is the same whether they marry using a civil or a religious form of ceremony.
"Arguments that seek to treat 'religious marriage' as being a different institution fail to recognise the enduring place of the established church in providing marriages that have full state recognition."
The Church of England said it would submit a more detailed response before the end of the consultation in around 12 weeks' time.
It added: "The Church of England will continue to argue against changing the definition of marriage, which has supported society for so long."
The Government has stated that the consultation is not about whether to legalise gay marriage, but about how it will implement the change.
Its push to introduce same-sex marriage has been strongly criticised by Church leaders.
A petition launched by the Coalition for Marriage in opposition to the plan has been signed by more than 230,000 people.