They will have to find a combined total of more than £7 million a year, instead of £5 million as originally forecast, according to documents published alongside the Non-Domestic Rates (Scotland) Bill.
This could mean smaller, rural schools have to pay bills worth about £500 to £600 per pupil, according to the Scottish Council of Independent Schools.
Critics of the Bill, which was introduced to the Holyrood parliament last week and is now under scrutiny by ministers, say the changes will curb independent schools’ ability to widen access to poorer pupils via bursaries. Fees could also rise and assets be sold off, they argue.
Liz Smith, the Conservatives’ education spokeswoman, said: “The SNP has, rightly, been at great pains to say that all schools should be much more inclusive and accessible to those from under-privileged backgrounds yet this proposed legislation would do exactly the opposite.
“It would make independent schools much more elitist and less able to offer the extensive bursary support which they have built upon over the last decade.
“The likely fee increases would push many pupils out of the independent sector into the state sector, which is already struggling to cater for the needs of the existing pupil numbers, and hard pressed Scottish taxpayers would have to foot the bill.”
Private schools are eligible for 80 per cent rates relief if they are registered as a charity, but this will end under the shake-up of business rates. State schools do not qualify for charitable relief.
Private special schools and specialist independent music schools would continue to be eligible for charitable relief under the legislation.
In a financial memorandum accompanying the new Bill, ministers said: “Mainstream independent schools will still retain their charitable status and other benefits will continue to flow to them from that status.”
Based on a starting date of 2020/21, the new rules would mean private schools have to pay £7 million extra in the first financial year. This would rise to £7.2 million the next year, £7.4 million the year after, £7.5 million in 2023/24 and £7.7 million the next year, taking account of inflation. In total, schools would pay £36.9 million more in the first five years.