Christian charities that promote particular versions of the faith, such as a traditional stance on sex, could lose their charitable status under new guidance, the Church of England has warned.

The established church believes there is a serious risk that dozens of charities could be affected by the Charity Commission's proposals to tighten up what constitutes a charity.

Earlier this year the commission published new guidance on what constitutes "public benefit", including on how religious charities must show they contribute to the public benefit. Under the same guidelines, many public schools are having to raise fees to pay for bursaries and other schemes to prove they benefit the poor.

Although the commission has made clear that it would only remove charitable status from an organisation as a last resort, the Church of England still believes there are grounds for concern. There are many thousands of church charities. Every parochial church council in the country is a charity, and there are more than 13,000 those alone.

Under the Gift Aid scheme, these charities gain many hundreds of pounds a year in reclaimed tax on donations.

The Church is concerned that charities with narrow objectives, such as promoting a traditional sexual ethic, might be unable to prove public benefit.

They are also objecting to the demand that pastoral work carried out by charities should be distinguished from purely secular or social work. In a society where faith-based providers of social welfare services are increasingly required to suppress their religious character, this would make their task even more difficult, the Church says.

"We are not aware of any legal basis for that proposition and would wish to argue strongly that what matters is the motivation of activity of this kind rather than what badges are attached to it in practice," the Church says in its response to the guidelines, published today.

At national level the Archbishops’ Council, which exists “to co-ordinate, promote, aid and further the work and mission of the Church of England”, is also a registered charity. The great bulk of the assets of the Church at the national level are held and administered by the Church Commissioners, a statutory body created by an Act of Parliament and which, having hitherto been an exempt charity, will in future be required to register.

Stephen Parkinson, spokesman for Forward in Faith, a charity that lobbies for traditionalists in the Church of England, said: "Of course we are concerned. It would be very hard for most church charities to demonstrate public benefit to the public at large. If we lose charitable status our income would be cut by about £30,000 a year."

The Prayer Book Society said they had taken advice and were content that they fell in within the demands of what constitutes public benefit.