The Church of England has said it was not properly consulted on a plan to ban it from conducting gay marriages.
Government officials had not disclosed details of their plans when they met Church officials, the spokesman said.
The Department for Culture, Media and Sport said it had been "quite specific" on planned protections for religious groups opposed to gay marriage.
The Church of England and Roman Catholics, among other denominations, have voiced opposition to same-sex marriage and are expected to oppose the government bill allowing it, even with the protections included in it.
In a statement to the House of Commons on Tuesday, Culture Secretary Maria Miller announced a "quadruple lock" of measures to protect religious freedom, including an explicit ban on the Church of England and Church in Wales performing same-sex marriage ceremonies.
On the previous Friday, Prime Minister David Cameron had announced that he wanted gay people to be able to marry, but that no organisation opposed to the move would be forced to conduct the ceremonies.
The day before the PM's remarks,
CofE officials had met for talks on the issue with officials from the
Department for Culture, Media and Sport (DCMS).
Meanwhile the Archbishop of Wales, Dr Barry Morgan, said he thought the ban was a "step too far".
"I'm not saying that the Church in Wales is ready to conduct gay marriages, but it ought to be in a position to decide that for itself," he told BBC Radio 4's World at One.
The government's thinking was probably that it needed to protect the established Church with a law prohibiting gay marriages to avoid possible legal challenges, he said.
"But all that was done without any consultation at all - it came as a total shock to us.
"I think some of us would want to argue that there's got to be a way round this legally, without making it a criminal act to hold such marriages in church if we so wish."
Senior level
The CofE spokesman said there was no wish for "protection or exemption for ourselves in ways that are any different from any other Church", though it was accepted that its unique position as the established Church would require particular legislation.
"If, despite our opposition, the legislation goes through, we support the government intention of leaving the choice of conducting same-sex weddings with all churches and faiths."
In a statement, the DCMS said: "It is just not true to say that we have not properly discussed our proposals with the Church of England. As part of our consultation process, and before we finalised our proposals, Government officials met the Church of England at a very senior level. The Church made clear to us its wish to see legal provisions which would ensure that their position on not conducting same-sex marriages could continue. While it is inappropriate to share the exact nature of legislative proposals before announcing them to Parliament, discussions with the Church were quite specific about the quad lock."
The Catholic Church in England and Wales has said that the process of formulating the policy "can only be described as shambolic".
"There was no electoral mandate in any manifesto; no mention in the Queen's Speech; no serious or thorough consultation through a Green or White Paper, and a constant shifting of policy before even the government response to the consultation was published," said a statement from Archbishops Vincent Nichols and Peter Smith, president and vice-president of the Catholic Bishops' Conference of England and Wales.