MPs have called for an inquiry into the Charity Commission because of its decision not to register the Plymouth Brethren as a charity.
The commission recently declined to register the Preston Down Trust, which runs a Brethren meeting hall which until the passing of the Charities Act 2006 was an excepted charity – one regulated by but not registered with the commission.
The trust has appealed to the charity tribunal against the decision.
During a Westminster Hall debate attended by more than 40 MPs yesterday, several said this was a case of discrimination against religious organisations.
Robert Halfon, Conservative MP for Harlow, said "there is something rotten in the Charity Commission" and that he could not understand why the Brethren had been singled out.
"I believe an inquiry is needed into the role of the Charity Commission to consider how it came to make the decision and to publish all the emails and correspondence – everything that led to the decision," he said.
Ian Paisley Jr, Democratic Unionist MP for North Antrim, called on Nick Hurd, the Minister for Civil Society, to take action to ensure the commission changed its views.
"The house is standing up for the little fellow as he looks down the barrel of the gun of the big fellow who is nothing more than a bureaucratic bully with his views on religious faith," he said. "Will the Roman Catholic Church face being bullied and browbeaten by the Charity Commission? I hope not.
"I also hope that the minister is listening, because this is the thin end of the wedge. He must take a stand, and do so now."
Hurd defended the commission, saying that it had a very difficult job. "There were concerns that the Charity Commission is pursuing an anti-Christian agenda," he said. "I am satisfied that that is not the case.
"The Charity Commission continues to register hundreds of Christian charities each year, including charities that were previously excepted. That fact has to be reconciled with various statements – some of them quite wild – about the commission discriminating."
He said it was for the courts to decide whether it was correct in its decision, and that it was not the role of the Cabinet Office to get involved.
Paul Flynn, Labour MP for Newport West, said the problem had not been caused by the commission, but by parliament.
"The difficulty is that we as a house failed to define public benefit in the Charities Act 2006," he said. "It is left to the courts. What will happen is that those who can afford the most expensive silks to argue their case are likely to triumph."