The move was greeted with dismay by Ewan Aitken, education spokesperson for the Convention of Scottish Local Authorities, who said councils had "serious reservations" about what amounted to a cut in resources from the Executive to the SQA being passed on.
"We will need to be convinced that we are getting a much better service from the SQA before we even start discussing these charges," Mr Aitken said.
Fees have held steady for the past four years after the exams meltdown in 2000 but since then the runaway success of the Higher Still reforms has increased costs way above expectation.
The authority has revealed a 240 per cent rise in the number of courses at various levels, including Access and Intermediate, which in turn has pushed up costs.
The impact of more courses with more units and more external marking together with higher fees for markers has raised the yearly deficit, which now runs to pound;18.4 million. The cost of markers, moderators and exam committees is around pound;14 million, out of an SQA turnover of pound;46 million.
Ministers want to ease the authority towards financial break-even over a number of years and have approved the fee increases which will fall on local authorities, further education colleges and independent schools.
The SQA hopes to raise an extra pound;6 million a year.
Anton Colella, its chief executive, said that the increases would lessen the dependency on Scottish Executive grant. "We are now starting to remove ourselves from the need for annual direct deficit funding, bringing us closer to the point of financial break-even ," Mr Colella said.
He said that the authority would also be looking at internal cost-cutting but pledged that quality assurance procedures would not be sacrificed.
Mr Colella continued: "When you compare SQA with elsewhere in the United Kingdom, our future charges are much lower and therefore represent good value for money."
Figures released by the SQA show that the cost of a Higher, Intermediate and Advanced Higher will rise from pound;23.75 to pound;32.75 per student in 2005-06. The authority points out that an AS-level course run by Edexcel, the largest examining body south of the border, already costs pound;33.
The cost of National Qualifications will rise by 20 per cent from next August, followed by 15 per cent the year after. Over the same period, Higher National Qualifications costs will rise by 5 per cent and 5 per cent. Scottish Vocational Qualifications will increase by 20 per cent and 15 per cent, matching the cost hikes of Highers.
Meanwhile, the costs of Standard grades will rise from pound;19.75 to pound;27.25 over two years.
Jim Anderson, education director in Angus and president of the Association of Directors of Education in Scotland, said councils and schools would be "anxious" about how they could afford the rises. In his own council, the extra in the first year alone will be pound;68,000. Fees for exams are already devolved to schools.
Mr Anderson said: "We would expect our budgets at council level to be enhanced. If not, then it will have to come out of something else in education."
He described the hikes as "pretty significant" at a time when all local authorities are beginning to introduce maintenance allowances to encourage more young people to stay on in education.