The Church of England and Church in Wales will be banned in law from offering same-sex marriages, the government has announced.
Other religious organisations will be able to "opt in" to offering ceremonies, Culture Secretary Maria Miller told MPs.
David Cameron has said he wants churches in England and Wales to be part of the plans.
But Mrs Miller said they had strong opposition and would not be included.
Labour, which is backing the government's plans, applying to England and Wales, urged ministers not to be "too reserved" in promoting the changes.
The Church of England and Roman Catholics, among other denominations, have voiced opposition to same-sex marriage.
But some religious groups, including Quakers, Unitarians and Liberal Judaism, are in favour.
In her statement, Mrs Miller promised a "quadruple lock" to protect religious freedom, involving:
*No religious organisation or individual minister being compelled to marry same-sex couples or to permit this to happen on their premises
*Making it unlawful for religious organisations or their ministers to marry same-sex couples unless their organisation's governing body has expressly opted in to provisions for doing so
*Amending the 2010 Equality Act to ensure no discrimination claim can be brought against religious organisations or individual ministers for refusing to marry a same-sex couple
*The legislation explicitly stating that it will be illegal for the Church of England and the Church in Wales to marry same-sex couples and that Canon Law, which bans same-sex weddings, will continue to apply
Mrs Miller said the Church of England and Church in Wales had "explicitly stated" their opposition to offering same-sex ceremonies, so the government would "explicitly state that it will be illegal for the Churches of England and Wales to marry same-sex couples".
She also said: "I am absolutely clear that no religious organisation will ever be forced to conduct marriages for same-sex couples, and I would not bring in a bill which would allow that.
"European law already puts religious freedoms beyond doubt, and we will go even further by bringing in an additional 'quadruple legal lock'. But it is also a key aspect of religious freedom that those bodies who want to opt in should be able to do so."
Plans to legalise same-sex marriage have divided the Conservative Party and more than 100 Tory MPs are thought to be against the idea.
One of these opponents, Peter Bone, asked the Commons: "How dare the secretary of state try to redefine marriage?"
But a number of senior Tories including Education Secretary Michael Gove, London Mayor Boris Johnson and former Prime Minister John Major have backed same-sex marriage by religious bodies.
Ben Summerskill, chief executive of the gay rights organisation Stonewall, said: "We're delighted about the government's statement today and welcome the promise to legislate for equal marriage as warmly as on the three previous occasions that this announcement has been made.
"We're particularly pleased that ministers have been persuaded to extend their original proposal in order to permit same-sex marriages for those religious denominations that wish to hold them. This is an important matter of religious freedom."