It is likely to mean a bill of almost £37 million over the next five years as ministers move to end charitable relief from the institutions.
It had initially been estimated that the independent sector would be hit with a £5 million a year bill, but that is likely to be more than £7 million a year, according to documents published alongside the Non-Domestic Rates (Scotland) Bill.
“The idea that independent schools are full of the super-rich is simply not true. All of this money comes out of parents’ pockets," he told the Herald newspaper.
"These schools are not-for-profit.”
It could now result in fees going up, playing fields and other assets being sold off, as well as cuts to teacher numbers and grant funded assistance for poorer youngsters.
Based on a commencement date of 2020/21, ministers said the new rules would see private schools forced to pay £7m extra in the first financial year.
This would rise to £7.2m the following year, £7.4m the year after, £7.5m in 2023/24 and £7.7m the next year, taking account of inflation. In total, schools would pay £36.9m more in the first five years.