Boys beat girls and face investigation
But there is speculation that the inclusion of science questions - part of a revamp designed to make the test reflect work being done in the classroom - may have skewed the papers in favour of boys.
The Council for Curriculum, Examinations and Assessment denied the swing was of any real significance and many teachers argued it could be a "blip" for one year.
But the department said it wanted to examine the spread of results to ensure that the tests had been fair. Education minister Michael Ancram said: "Our main responsibility is to make sure that the test is fair so that pupils and their parents can have confidence in it."
Tom McKee, regional secretary of the National Association of Schoolmasters Union of Women Teachers, called for a fundamental review of the whole procedure which has been dogged by controversy for years.
Until three years ago, the papers were based on verbal reasoning which became largely discredited and seemed to favour girls because of their advanced language development at 11 compared to boys.
Meanwhile, scores of teachers in the province are facing redundancy as a result of budget cuts in schools, more than 100 in one of the province's five border areas alone.
The crisis is the result of the first year of the implementation of the Government's decision to transfer funds to all schools operating in areas of social disadvantage.
Many schools are facing financial reductions of between Pounds 65,000 and Pounds 100,000 and boards of governors are opting to make staff redundant. The department, however, said that the overall pupil teacher ratio in the province, particularly in the secondary sector, was improving.