Lord Alli proposed the amendment to the Equality Bill
Traditionalist Christians have appealed to ministers to block plans allowing civil partnership ceremonies to take place in churches.
They are worried that new laws, part of the Equality Bill, will mean clergy could be be prosecuted if they refuse to carry out the ceremonies.
Currently gay partnerships cannot be registered in places of worship.
The government has said the ceremonies are voluntary and no-one will be prosecuted for refusing to hold them.
However, critics say that the change is another attempt by gay campaigners to elevate civil partnerships to the same status as marriage.
Christian groups have presented a petition to the Equalities Minister, Harriet Harman.
It calls on the government to "listen to the large proportion of the electorate who perceive the government's acceptance of this amendment as a further attempt to progress so-called 'equality' today, while ultimately compromising tomorrow's 'religious freedom'".
Currently, gay couples cannot register their partnerships in places of worship
Andrea Minichiello Williams, from the group Christian Concern for our Nation, said that priests who refused to allow their churches to be used for the ceremonies could find themselves under investigation by the police.
She pointed out that Christian registrars have lost their jobs after refusing to register same-sex civil unions.
"How long will it be before church ministers are threatened with legal proceedings if they perform marriages between a man and a woman, but not civil partnerships?" she says.
Laws permitting civil partnership ceremonies in churches were approved by the House of Lords at the beginning of March. Peers voted in favour of Lord Alli's amendment by 95 votes to 21.
The Government has insisted religious organisations will not be forced to act against their beliefs.
The Quaker and Unitarian Churches, and liberal Judaism have supported the ceremonies, saying it would allow them to welcome gay and lesbian couples wanting to celebrate their commitment to each other, in the same way as heterosexual couples could in a church or synagogue wedding service.
The legislation has yet to be passed by the House of Commons, but the petition is the latest move in a long-running battle over ethics between religious conservatives and the Government.
Religious groups have been in the forefront of attempts to block any watering down of laws prohibiting assisted suicide.
And Catholic bishops in England, Wales and Scotland are still angry after losing a battle to try and exempt their adoption agencies from new rules requiring them to consider gay couples as potential adopters.
The BBC understands that the Liberal Democrat peer Lady Williams tried to introduce a further amendment to the Equality Bill which would have reversed this ruling, allowing Catholic adoption agencies to continue to 'act according to their conscience'.
However, her proposal was ruled 'out of order' by Lords authorities on Monday evening.