In an interview with The TES Scotland, Judith Sischy said that the proposed changes to charities law were "reasonable".
"If you receive public benefit, you are duty bound to give back public benefit," Mrs Sischy said. "Our schools give back easily what they receive and probably many, many times more."
The public benefit criteria, contained in section 8 of the Bill, were complex and the Office of the Scottish Charity Regulator would have to consult with the sector on how to interpret the practicalities, Mrs Sischy said.
As currently worded in the Bill, the regulator would have to weigh the public benefit provided by a body against any disbenefits. On that basis, she thought, no independent school would fail the test because she did not believe they provided a disbenefit.
The regulator would also have to look at whether there were any "unduly restrictive factors" in the public benefits offered. If this posed a problem, the regulator would say to a school that to stay on the charities register it would have to look at various factors, and the school and regulator would take things from there, Mrs Sischy said.
"It is theoretically possible that a school might not meet the criteria but I don't see it happening."
Mrs Sischy warned, however, that the first hurdle for the independent sector was to get through the political debate as the Charities and Trustees Investment (Scotland) Bill entered stage one of the legislative process.
Already Tommy Sheridan, Glasgow MSP, former leader of the Scottish Socialist Party and self-styled "class warrior on the side of the working class", as he described himself in last week's parliamentary debate, has called for a presumption against independent schools enjoying charitable status and the accompanying tax benefits.
Fettes College, with boarding fees of pound;20,199 a year, was "a glorified child-minding agency", Mr Sheridan said. The people of Scotland wanted an end to "the ridiculous situation in which such elite institutions are able to hide under the cover of charitable status".
The SSP sought to amend the legislation so that only independent special schools could receive charitable status, while the Scottish National Party wanted an organisation to show that its "overriding purpose" was to provide public benefit. Both amendments failed.
Christine Grahame for the SNP said: "The catch-all part of the SNP amendment would give flexibility to the Office of the Scottish Charity Regulator (OSCR), which is necessary in the grey areas that will arise in practice."
She added: "I will be blunt. The Gordonstouns and Fetteses of this world represent an exclusivity that would fail the test, while Donaldson's College for the Deaf is at the other end of the spectrum. There are grey areas in between."
But Karen Whitefield, Labour convener of the communities committee which has been scrutinising the legislation, said: "For the first time, organisations will not automatically qualify for charitable status just because they provide education. Such organisations will need to convince OSCR by proving and demonstrating that they meet the criteria in the Bill, against which OSCR must judge whether they are charities."
Mrs Sischy said: "Ministers have already said that they will look at issues such as scholarships and bursaries, making schools open to the local community and their contribution to the local community beyond their own school.
"I don't think it will be a question of whether a school offers two, 10, 50 or 100 scholarships but looking at a community within a community - what are you doing for the public here?"
She added: "The regulators will do this well - they are professionals and they will have to look at the whole picture.
"Our members care about being professional too. They have always been charities and would like always to be charities - more than the fiscal benefit, this is what it means to them. For far longer than any of us can remember, they have always done good deeds but didn't always look for headlines.
"Now they will have to demonstrate that to the regulator, but I don't think they will have a problem. No school is a selfish organisation. You can't be in a school and be selfish. All schools contribute to the community."