School leaders are urging the education minister to restore `freedom of choice' following a decision by English awarding bodies to stop offering GCSEs in the north.
Two boards in England - the AQA and OCR - both said they would not be offering reformed GCSEs in Northern Ireland.
Familiar A*-G grades are to remain in place for GCSE pupils with the north refusing to follow England in adopting a numerical system.
Education minister John O'Dowd consulted on changes following England's move to numerical grading from 2017. Grading in Wales will continue to be alphabetical.
Mr O'Dowd told the assembly that there were no educational arguments for changing to numbers.
Members of the assembly education committee voiced concerns, however. They fear pupils receiving grades on the A*-G scale will be at a disadvantage when applying for some university places in future.
Most pupils take exams offered by the north's exams board, the CCEA. However, many take papers set by boards from England too.
The minister had told awarding bodies that they would have to continue to use the A*-G grades.
The OCR board said it had developed 37 new qualifications for first teaching from 2015, and 47 new qualifications for first teaching from 2016. Following Mr O'Dowd's decision, it said, there were significant structural differences between GCSEs across England and the north.
"OCR therefore reached a difficult decision which is disappointing news for schools and colleges," it said in a statement.
"For operational and financial reasons, we regret that we are not able to offer qualifications specific to Wales or Northern Ireland, alongside a large portfolio of different, reformed qualifications that we have developed for England.
"Wherever we still have the opportunity, we will continue to offer the English versions of qualifications in Wales and Northern Ireland."
The AQA said it too had considered its position.
"We've decided not to adapt certain new qualifications for Northern Ireland. We're sorry about this: we know that schools and colleges in these countries will be disappointed," a spokesman said.
"It was a difficult decision to make: we'd like all our qualifications to be available to everybody. But we had to consider the practicalities of running significantly different versions of the same qualification - including the extra administration needed, and the challenge of trying to set the same standard across different countries.
"We've informed the Department of Education Northern Ireland that we will not be offering reformed GCSEs in Northern Ireland. We've asked that they make some transitional arrangements for students who have already embarked on an AQA English or maths course for assessment in 2017, so that they will not be disadvantaged by having to change mid-way through a course of study," a spokesman said.
The Association of School and College Leaders (ASCL) Northern Ireland said the announcements by AQA and OCR, effectively meant an end to the open market in which qualifications were available from those boards, as well as the CCEA.
"Given that over 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," said Robin McLoughlin, ASCL Northern Ireland president.
