The government has been accused of "rail-roading" through gay equality laws that, Catholic adoption agencies argue, will force them to close.
Cardinal Murphy-O'Connor said there should be a full Commons debate
Some Tory MPs criticised the "unseemly haste" with which ministers sought to pass regulations through Parliament.
Roger Gale said the rules had gone through "on the nod", adding: "That is not the way Parliament should be handling highly contentious business."
But Equalities Minister Meg Munn said standard procedure had been followed.
The Equality Act (Sexual Orientation) Regulations are aimed at outlawing discrimination against gay people by businesses and service providers.
The Catholic Church says they mean it will have to shut its agencies, which handle some of the most difficult-to-place children, rather than act against its beliefs. It has been given 21 months to adjust to the new rules.
But Tory backbenchers have complained that a deal between the government and their own front bench, has left little room for debate.
Mr Gale said it had gone through "at a very early hour last Thursday morning, in a very small committee room, with very few members present."
Then he said it had appeared as the last item of business on Monday - when most MPs were not in the House.
"It is clear that to this extent there was an unholy alliance between the Opposition front bench and the government front bench, that they decided it would go through in this form," he said.
The draft regulations were debated in a 90-minute committee meeting but did not have to be debated by MPs, because they formed part of the Equality Act - two thirds of which has already been approved.
"It's just not true that the process was anything out of the ordinary," Ms Munn told BBC Radio 4's World at One programme.
"We would have been happy as a government to have this on the floor of the House of Commons."
But she said the Opposition had not requested it,
"What we have got is people who don't like the decision, complaining about the process."
An attempt by backbench Tory MPs to get the regulations thrown out on Monday was defeated, by 310 votes to 100.
Many flooded into the Commons chamber on Monday evening to raise a series of points of order about the way the regulations were being handled.
'Abuse of democracy'
Tory former home office minister Ann Widdecombe said there had been an "almost unprecedented shortness of time" from the regulations being introduced and moved into the Commons.
Mr Gale, who complained the regulations were being "rail-roaded" through, said he hoped the vote would send a message to the Lords, to reject the regulations during their debate on Wednesday.
Lib Dem MP Evan Harris, who supports the new regulations, also said he was concerned they were being rushed through without proper debate.
Earlier the Catholic head of England and Wales, Cardinal Cormac Murphy-O'Connor, has also accused the government of "an abuse of parliamentary democracy" for rushing through the regulations.
A cross-party working group has been set up to liaise with the Catholic Church to try to find a compromise and a way to allow Catholic agencies to keep working under the new law.