Almost every pupil at a Dublin grinds school has had at least one grade reduced in the Leaving Cert with 96% affected.
The Institute of Education, home to the largest number of Leaving Certificate students in the country with over 800 enrolled, said its students have been "significantly penalised" by this year's calculated grades process.
Almost half - 44% - of all grades estimated by its teachers were reduced in the national standardisation process while the equivalent national average was 17%.
These grade reductions affected 96% of the student body "some worse than others".
The Institute, based on Dublin's Leeson Street, said it commissioned an analysis that found a "serious flaw" in the model used by the Department of Education.
It is calling for the appeals process for students to be widened.
Ms Yvonne O’Toole, principal of the Institute of Education, said: "The endemic flaws in this process have resulted in 96% of our students having a grade reduced.
"This level of reduction, along with a national grade inflation of 4.4%, will result in hundreds of our students missing out unfairly on their chosen careers tomorrow when the CAO offers are made."
She said the school had written to the Taoiseach and relevant Ministers today asking them for an appeals system that allows the calculated grades given to be challenged.
Ms O'Toole said students of the Institute should not be penalised in tomorrow’s CAO process because no redress system was in place to take account of what she called "the flaws in the State methodology".
The school said that, year on year, its students "significantly outperform" the national average in the Leaving Certificate exam.
It claimed the standardisation system was biased against larger cohorts of students, as is the case in the Institute.