Religious charities benefiting from generous tax breaks are promoting beliefs and activities which run counter to British values and opinion, according to new analysis.

For the public benefit? a report by the National Secular Society, finds that more than 12,000 British charities now exist solely to promote religion.

It claims that some are using their positions to push controversial views, including several Christian ministries which promote “gay conversion” therapy and those that promote the non-stun slaughter of animals for halal and kosher meat. It raises similar questions about charities that promote sharia courts and beth dins – councils which rule on matters involving disputes in the Islamic and Jewish communities respectively.

The society argues such activities can have a fragmentary effect on British society. Its chief executive officer, Stephens Evans, has written to the chair of the Charity Commission, Baroness Stowell, calling for a re-think on whether such organisations should continue to qualify for charitable status.

“Not only has religion ceased to be the force for social cohesion that it once was, the rise of religious fundamentalism has also demonstrated how religion can exacerbate tension, division, segregation and conflict in Britain,” Evans writes. “As such, we believe there is a clear need now to consider whether the advancement of religion should be regarded as an inherent public good, deserving of the status of a charitable purpose.”

The report suggests many religious charities are politicised. It cites the examples of several whose members have been shown to promote extremist views.

“Charities cannot take their privileged place in society for granted,” Evans said. “They must show they deserve it. 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.”

Nearly half of all UK overseas charities are faith-based, the report finds. Around 30 are now supported by the government compared with only two a couple of years ago, according to the society, which warns that some Christian charities have used poverty and humanitarian tragedies as a means to evangelise to children, often in Muslim-majority countries.

More than a quarter of the religious charities that enjoy an annual income of over £10m exist solely to promote their religion, the analysis finds.

“Advancing religion is not an unqualified good,” Evans said. “In some cases it has no public benefit and in others it is actively harmful. Religious organisations that wish to be registered as charities should be required to demonstrate that they serve a genuine public benefit under another charitable heading, for example because they alleviate poverty.”

Dan Corry, chief executive of New Philanthropy Capital, which offers advice to charities, said many of the UK’s most illustrious charities had been founded by religious groups and that the relationship between both sectors was entrenched.

“Some of them only work with people of their faith, some are very inclusive. Most people are happy with religious charities. Interestingly, they often work with people who no one else will work with. But there will always be some who really should not be classed as a charity.”

A Charity Commission spokeswoman said: “We are aware of the National Secular Society’s report on charity and will review it carefully. As a general principle: 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.”

• This article was amended on 19 March 2019 to clarify that the report refers to charities that support the non-stun slaughter of animals for halal meat and for kosher meat.