An independent report commissioned by the exam board concluded that candidates who took its statistics papers could have been disadvantaged because some questions were seriously flawed.
The board has withdrawn five sets of past papers from circulation to ensure that no more schools use them in the classroom. Schools which already have the papers are to be sent guidance highlighting the board's concerns.
The decision comes after a long-running row between the board - the Council for the Curriculum, Examinations and Assessments - and one of its former exam-question scrutineers, who believes that every statistics paper since 1997 has contained serious errors.
Former head of mathematics at Belfast Royal Academy, James Nicholson, said:
"There have been mistakes in sven successive sets of papers since 1997."
As a result of his concerns, the board commissioned a report from Gerald Goodall, an independent statistics examiner, who supported many of the criticisms.
He concluded: "Candidates might have been disadvantaged in the examination room, due to not knowing how to answer a flawed question. It is a serious matter that badly flawed questions, and flawed solutions, will have entered the public domain through the normal processes of publication."
The board's two statistics modules have become increasing popular options within A-level maths: more than 900 sixth-formers sat them last summer, up from 680 in 1997.
The board maintains that no candidate has been disadvantaged and that the highly technical nature of Mr Nicholson's queries does not invalidate the use of the questions for A-level. However it has tightened procedures surrounding the statistics modules.