The Executive has been urged to intervene after Education Minister John O'Dowd refused to reverse a decision that caused two English exam boards to pull out of Northern Ireland.
The AQA and OCR said they could not offer two grading systems after Mr O'Dowd declined to introduce the numerical system set for England, saying he would stick with the letters format.
DUP education committee chairman Peter Weir urged Mr O'Dowd to reconsider his decision, but the Sinn Fein man rejected his plea.
Afterwards, Ulster Unionist MLA Sandra Overend called for the Executive to intervene and said: "The decision to retain the alphabetical grading system was wrong and our students are going to be disadvantaged.
In response, Mr O'Dowd expressed disappointment at the exam boards and said: "Some organisations are choosing to put commercial interests ahead of the needs of our young people."
TUV leader Jim Allister claimed there was a clear conflict of interest. "Divergence from the system in the rest of the UK fits the minister's republican agenda," he said. "It does not, however, make sense for students or teachers. Schools now have a much reduced choice. Additionally, courses which have been taught for years and the resources purchased to teach them have been rendered obsolete.
"We now have a situation in Northern Ireland where the regulator (the CCEA) is also the sole provider of examinations.
"Young people who move to other parts of the UK for employment or further eduction will now face problems explaining what their qualifications mean."
The row came as a survey by the Association of School and College Leaders (ASCL) found the vast majority of school leaders disagreed with Mr O'Dowd.
ASCL Northern Ireland president Robin McLoughlin called on the minister to restore freedom of choice and added: "When the minister's decision to require English awarding bodies to conform to the A*-G grading system was taken, ASCL warned that it would not be possible for an open market for qualifications to be maintained. It now appears this will be the case.
"Given that more than 40,000 GCSE examination entries in Northern Ireland each year are with English awarding bodies, we ask that the minister restores the freedom of choice promised to pupils to choose the qualifications best suited to their future career choices and allow both Northern Ireland and English GCSE examinations to continue to be offered here as at present."
But Mr O'Dowd said: "(Work is) well under way to ensure that our young people can continue to access the widest possible range of subjects and courses, including those most relevant to the needs of our economy, to progress on their chosen path in learning or employment.
"I also want to assure them of my commitment to ensuring that our young people have access to a broad and relevant curriculum, supported by internationally recognised qualifications."
Mr O'Dowd added that schools would be advised on the next steps at the end of this month.