More than 5,000 GCSE students were sent the wrong results, about a sixth of the total number of candidates.
But no one knew which had received incorrect print-outs and so all 31, 000 students were forced to verify their results with the schools.
Michael Ancram, the education minister, has demanded a full inquiry and a preliminary report was due this week.
The initial explanation appeared to be a simple slip-up after out-of-date stationery was loaded into the computer system.
The effect was that many students received grades for examinations in subjects they had never taken while thousands of others faced agonising waits while schools received the correct results only to find they had fared worse or better than they first thought.
The newly-merged Northern Ireland Council for the Curriculum, Exams and Assessment, which is due to take over the full running of the 11-plus in the new school year, issued an abject apology and pledged the blunder would never happen again.
But parents and teachers said the slip-up was incredible coming after the leaking of questions in the 11-plus transfer exam which led to 18,000 children being forced to sit a third paper and an inquiry into two physics papers based on separate syllabuses which contained some identical questions but were timetabled for different dates.