Education Minister John O'Dowd briefed MLAs on discussions with his southern counterpart on the non-acceptance of Northern Ireland qualifications by universities in the Republic, on 23 October 2012.
Mr O'Dowd was reporting back to the Assembly on a recent North South Ministerial Council (NSMC) meeting on education.
He said he understood that the CAO (Central Admissions Office) would only allocate points in respect of A Levels taken in the same year, meaning that pupils taking A Levels a year early would be at a disadvantage.
"I feel this system is unfair and have asked CCEA (Council for the Curriculum Examinations and Assessment), as the qualifications regulator in the north, to raise this with the CAO," he said.
The minister also noted that Applied A Levels and BTECs were not recognised by Irish universities.
The UUP's Danny Kennedy, speaking for the education committee, expressed "the committee's growing concern at this issue".
The minister said he was happy with the response shown by the Irish Education Minister, Ruairi Quinn, on the matter but "the body we are dealing with is independent and will take its own counsel".