A bill to legalise gay marriage is being published by the Government.
The legislation is likely to provoke ferocious debate in the House of Commons, where a significant number of Conservative MPs are opposed to same-sex marriage.
But Culture Secretary Maria Miller insisted it would ensure "equal and fair" treatment of gay couples, while providing adequate protection for religious institutions which do not want same-sex weddings to take place on their premises.
Mrs Miller told BBC Radio 4's Today programme: "We feel that marriage is a good thing and we should be supporting more couples to marry and that is exactly what the proposals being brought forward today do.
"But it is about making sure that not only do we recognise the rights of same-sex couples in civil life, but we also recognise that some churches won't want to participate in same-sex marriages.
"We are trying to make sure that there are the protections there for churches who feel that this isn't appropriate for their particular beliefs. We know that there are churches who do want to take part in same-sex marriages, so we have made sure that there are provisions there so they can."
The legislation sparked controversy after it emerged that a "quadruple lock" designed to protect religious institutions from being forced to conduct gay marriages against their wishes will make it illegal for such ceremonies to be conducted by the Church of England and Church in Wales.
Mrs Miller said: "At the end of the process, there will be the same freedoms there for the Church of England and Church in Wales, but they have to be achieved differently, because the Church of England and Church in Wales have a common-law duty to marry people, and that is quite different from any other religious institution in the country. Therefore you would expect there would have to be slightly different provisions there."
She added: "I don't think it is for any government to tell the Church of England what they do when it comes to something which is so central to religious belief."
David Cameron has given Conservative MPs a free vote on the Bill.