The advancement of religion should be scrapped as a charitable purpose, the National Secular Society has claimed.
Its report For the Public Benefit? says 12,000 charities in England and Wales currently exist solely to promote religion.
The report calls for them to lose their charitable status unless they can fulfil one of the 12 other charitable purposes listed in the Charities Act 2011, such as the advancement of education and the relief of poverty.
Stephen Evans, chief executive of the society, said advancing religion was not an "unqualified good" and removing it was "overdue and in the public interest".
Evans added: "In some cases it has no public benefit and in others it is actively harmful.
"Too many faith-based charities are causing harm at the expense of the taxpayer.
"Tax breaks are allowing these organisations, under the guise of ‘charity’, to facilitate harmful activities that do not align with British values and opinion."
The report says some religious charities promote activities such as "gay conversion therapy", infant circumcision and non-stun animal slaughter.
It adds that other religious charities are "highly politicised" or hold extremist views.
And it cites the Charity Commission's refusal to register the Pagan Federation, the Church of Scientology and the Temple of the Jedi Order, which is based on fictional characters in the Star Wars films, as examples of the regulator's inconsistent approach to religion.
Evans said he hoped the report, which is based on data provided by the commission, would start a debate that would lead to a "shift in opinion over time".
Parliament set the 13 charitable purposes in the 2011 act. It is the commission's job to test for them.
A Charity Commission spokeswoman said it would review the report.
She added: "Like all charities, a small proportion of religious charities are misused by others and used in ways the public would not expect.
"The commission deals with these issues robustly where they arise."