The House of Lords has voted in favour of a change to civil partnership laws to allow gay couples to marry in churches and use religious language during the ceremony.

Peers voted 95 to 21 in favour of the amendment to the Equality Bill late last night, overturning a ban under the Civil Partnerships Act on same sex unions taking place in religious premises.

The move has prompted fears among some Christians that churches could be taken to court if they refuse to carry them out civil partnerships in their buildings and that the line between civil partnerships and marriage will be blurred.

The Evangelical Alliance said that although churches were still entitled to refuse to conduct civil partnerships, anti-discrimination laws under the Equality Act could undermine this protection and leave them confused about what they are allowed to do.

Dr Don Horrocks, Head of Public Affairs for the Evangelical Alliance, said: “We understand the Lords’ desire to allow a few liberal religious groups to have freedom to follow their consciences.

“But neither must other religious groups be forced to betray their consciences by facing lawsuits if they fail to allow a civil ceremony.”

Dr Horrocks said the amendment “hugely confuses” the nature of marriage and the distinction between civil secular ceremonies and religious ceremonies.

He warned it would have major implications for matrimonial laws “which haven’t begun to be thought through” and added that the balance of freedoms was not fair on Catholic adoption agencies.

“On the same night, the Government refused to allow Catholic adoption agencies liberty to follow their consciences, but the two decisions are contradictory and inconsistent,” he said.

“We don’t want to see in a few years’ time churches ending up in the same boat, where they are forced to comply with anti-discrimination law or close down.

“The Government therefore needs to make clear that no church will ever in the future be able to be successfully sued on grounds of discrimination for failing to allow a civil ceremony while it continues to permit religious marriages.”

The amendment, moved by homosexual Labour peer Lord Alli, had originally been resisted by the Government in January last year on the grounds that it was “not a workable solution to this issue”. In a surprise move, it allowed its peers a free vote on the issue, as did the Conservative Party and the Lib Dems.

The amendment was supported by the former Bishop of Oxford, Lord Harries, as well as Quakers and liberal Jews. Gay rights group Stonewall said the vote was a “victory for religious reason” over the “bullying” of some Church of England and Roman Catholic bishops who had opposed the amendment.

The Bishop of Bradford the Rt Rev David James, the only Church of England bishop present in the debate, voted against the amendment to ensure that religious people were “recognised” and “that others do not ride roughshod over what are deeply held and sincere sensitivities in terms of their lifestyles”.

Andrea Williams, director of Christian Concern For Our Nation, said the amendment “effectively removes one of the final distinctions between marriage and civil partnerships”.