Church of England clergy will be sued for discrimination if they refuse to “marry” homosexuals under a proposed law, a bishop has warned. Other religious leaders fear that churches that refuse to bless civil partnerships might be forced to close.

The Bishop of Winchester said the vote by peers to lift the ban on civil partnership ceremonies in religious buildings will blur further the difference between marriage and civil partnership. Since the change in the law signalled on Tuesday means that the Church will be allowed to conduct the ceremonies, but not be compelled to hold them, legal challenges could come under anti-discrimination laws.

The Right Rev Michael Scott-Joynt said: “I regret enormously the vote.” Referring to the Church’s continuing policy against holding civil partnership ceremonies, he added: “I believe that it will open, not the Church of England but individual clergy, to charges of discrimination if they solemnise marriages ... but refuse to host civil partnership signings in their churches.”

Peers voted by 95 to 21 in favour of an amendment to the Equality Bill by the Labour peer Lord Alli that will lift the ban on religious venues and language for civil partnerships.

Although the Government did not back the amendment, it is thought that Harriet Harman, the Leader of the Commons, who has been shepherding equalities legislation, will not wish to risk the entire Bill by sending it back to the Lords.

The Evangelical Alliance said that churches could be left in the same position as Roman Catholic adoption agencies, most of which have closed or dropped their religious ethos after being refused permission to discriminate against gay couples. The one surviving agency, Catholic Care, took its fight to survive to the High Court yesterday.

Don Horrocks, of the alliance, said: “We understand the Lords’ desire to allow a few liberal religious groups to have freedom to follow their consciences. But other religious groups must not be forced to betray their consciences by facing lawsuits if they fail to allow a civil ceremony.

“This amendment hugely confuses the distinction between civil secular ceremonies and religious ceremonies, as well as the nature of marriage, and has major implications for the UK’s matrimonial laws which haven’t begun to be thought through.”

Consultations are taking place in Church and Government on the way forward. Lord Alli told the Lords: “There are many gay and lesbian couples who want to share their civil partnership with the congregations they worship with and there are a number of religious organisations that want to allow gay and lesbian couples to do exactly that.”

Ben Summerskill, chief executive of the gay rights group Stonewall, said of the vote: “It will be warmly welcomed by lesbian and gay people of faith.” Derek McAuley, chief officer of the Unitarians, which with the Quakers and Liberal Judaism was seeking the change in order to be able to carry out religious civil partnership ceremonies, accused the bishop of scaremongering.

The religious think-tank Ekklesia welcomed the vote but called for an overhaul of marriage law. Symon Hill, associate director, said: “It is time for a legal change that allows people to enter into marriages or partnerships as a public, communal, and if important to them, religious commitment, with legal registration being separate.”

The Pope is among the religious leaders who have criticised Britain’s moves in the secular realm towards equal rights for all. The Lords victory for gay marriage came as the Catholic Bishops of England and Wales launched their pre-election document in London yesterday. The Archbishop of Westminster, the Most Rev Vincent Nichols, said the Pope believed greater equality was “right and proper”. He added: “I think what we see in our society at the moment is some of the difficulties of trying to unfold that into a legislative programme.”