Concern is growing that a rule change could threaten the charitable status of strictly Orthodox groups, costing them large amounts in tax relief.

It follows a decision by the Charity Commission to refuse registration to a Devon church owned by the Plymouth Brethren, a small Christian sect.

This week it emerged that the commission had written to the Attorney-General, Dominic Grieve, suggesting that Chasidic and “Messianic” Jews were among groups that could be affected by the rule change.

Jon Benjamin, chief executive of the Board of Deputies, has written to Mr Grieve to express his concern. He said: “Established religious institutions that have benefited from charitable status should not now be subject to unreasonable scrutiny, simply because the commission has decided to move the goalposts.”

The problem stems from changes made to charity law in 2006. Charities must prove they benefit the public. But the legal changes removed the presumption that promoting religion was a public benefit in itself.

The letter that surfaced this week — which was written two years ago by the commission’s director of legal services Ken Dibble to a senior official in the Attorney-General’s office — questioned the extent to which charitable status could be granted to groups whose members “have limited engagement with the public in their daily lives”.

As well as the test case involving the Brethren, the issue could also apply “where there are closed communities or exclusive groups”, Mr Dibble said.

The commission had identified a number of religious groups which could be affected, he wrote, including “Bruderhof, Amish, Mennonite; Messianic and Chasidic Jews; and possibly some Buddhist organisations”.

In 2012, the commission rejected an application for charity status from Preston Down, a congregation of the Plymouth Brethren, a sect founded in the 19th century with 16,000 members.

A spokesman for the Brethren, whose appeal against the decision is due to be heard by the Charity Tribunal in March, said that it had been “unfair and unreasonable” as the sect donated £1 million a year to external charities.

He added: “The discovery that it is the commission’s intention to target other small religious groups, such as Chasidic Jews, in the same way they have targeted the Brethren, should set alarm bells ringing in all religious communities.”

Lawyer Jo Coleman, who has briefed Charedi groups, said: “It was not Parliament’s intention to remove charitable status from existing religious charities and the tribunal will need to be aware of the wider consequences of any ruling it makes in March.”

William Shawcross, the commission chairman, said: “The issues concerning the Preston Down Trust… are specific to this particular organisation.

“The commission has not changed its approach to registering religious organisations, which we do according to charity law. I am well aware of the vital role that religious charities have played in British society for centuries.”