Amendments have been added to the Equality Bill to reassure clergy that they will not be sued if they refuse to hold religious civil partnerships for gay couples.

Although out gay peer Lord Alli and other supporters said the measures were permissive, some bishops and conservative Christian groups claimed they would lead to clergy being sued.

During the Equality Bill’s third reading in the Lords last night, Lord Alli said that the amendments would make it “crystal clear” that the change in the law was about religious freedom.

However, the changes mean that national churches may be able to prevent liberal clergymembers from performing civil partnerships, rather than the allowing the individual to choose whether he or she officiates the ceremonies.

Keith Porteous Wood, executive director of the National Secular Society, told the Daily Telegraph that the government had caved in to religious pressure.

He said: “The government bowed to pressure from the Anglican and Catholic hierarchy to give them legal backing to block liberal parishes from hosting civil partnerships.

“Without the amendment, the blessing of civil partnerships in churches could have become the norm, despite Episcopal disapproval.”

Speaking last night, Lord Alli said: “I very much hope that these amendments will give comfort to faith communities which have suggested that they will soon be forced to perform civil partnerships against their will. . . These amendments make crystal clear that this change in the law is entirely permissive in its approach.”

The bill passed its third reading, meaning it is likely to receive royal assent and become law before the general election.

However, further legislative changes will be needed to allow religious civil partnerships. The Civil Partnerships Act 2004 must be changed, as it states that the ceremonies may only take place in approved, non-religious premises and cannot contain hymns or prayers.

Baroness Royall told the House that the ceremonies would work in a similar way to religious heterosexual marriages. She explained that the ceremony itself could have religious references but these would not be allowed while the couple sign the register.

She said: “A civil partnership registrar will still be required to officiate the signing of the register, and it is correct that there can be no religious service during the civil partnership registration.”