Scotland could be left with a two-tier charity system if plans to strip independent schools of their tax breaks go ahead, according to internal Scottish government documents.
Last year's Scottish government-commissioned Barclay Review of Business Rates recommended that fee-paying schools should lose the 80 per cent discount on business rates awarded to charities. It said the relief was unfair because state schools did not receive it.
Derek Mackay, the Scottish Finance Secretary, backed the proposal in December, describing it as "fair and consistent".
But emails between civil servants in the Scottish government's charity law and volunteering team and officials at the Office of the Scottish Charity Regulator, revealed under freedom of information legislation, show widespread concerns about the proposal.
An email from the team on 8 June last year said: "It would essentially create a two-tier system for charities. We are not convinced that this would be desirable and it could be difficult to justify.
"Removing rates relief would mean that we were creating a class of charities who receive less favourable treatment.
"It sets a precedent for differential treatment of other types of charitable organisations further down the line."
Some correspondence also suggests that the abolition of rates relief would be better dealt with as part of a wider campaign to consider whether fee-paying schools should be charities.
It says: "If the real issue is whether these organisations should be charities in the first place, this would be better addressed by looking at, and potentially amending, the charity test in the 2005 charity act, rather than subjecting them to what is essentially a financial penalty."
The documents also contain several comments from principals and headteachers criticising the proposals.
Melvyn Roffe, principal of George Watson's College in Edinburgh, said: "It would be a bit perverse to end up with a bill, which in our case would be another £460,000 a year, and that would inevitably end up on the fees. If you want the schools to be more elitist, then the best way to do it is to lump on lots of extra costs and sure enough that will become more elitist – despite our best efforts not to."
A spokesperson for the OSCR told Third Sector: "The Barclay recommendations do not alter the charitable status of any of the affected charities, and we will continue to assess the potential impacts for charities and for the OSCR."