The decision has been welcomed by schools in England and Wales, who will also have to prove they are providing a public benefit following changes to the law.
They will have to show they are making places available to children from poorer families to retain charitable status, estimated to be worth pound;100 million a year in tax breaks.
The Office of the Scottish Charity Regulator said 14 of 16 charities taking part in pilots had passed its benefit test.
This included Dundee High School, for five to 18 year-olds, with fees up to pound;8,300 a year. The school developed new materials with the Scottish Qualifications Authority, opened its sports facilities to outside groups and provided places to trainee teachers, the regulator said.
The decision in Scotland is not binding on the Charity Commission for England and Wales. However, it was welcomed by Jonathan Shephard, general secretary of the Independent Schools Council.
"In terms of schools in England, this kind of approach seems to be straightforward and would pose no problems. It's certainly clear that schools providing public benefit have nothing to fear," he said.
The Charity Commission in England and Wales will publish its general guidance on public benefit in October and begin consultations with independent schools in November.
One of the charities that failed the test in Scotland was John Wheatley further education college, in Glasgow.
This is because charities in Scotland need to be independent from the control of Scottish political ministers.
However, most Scottish FE colleges have constitutions that give ministers powers, including the ability to close them down. The regulator has given politicians two years to resolve the problem.
Gordon Brown's new education advisers this week discussed how independent schools can help raise standards in state schools, at the first meeting of the National Council for Educational Excellence.