Notable falls in Higher passes at English and mathematics - 7.6 per cent and 4.7 per cent - may be partly attributed to students sitting inappropriate levels.
Ironically, the national drive to judge secondaries by the "gold standard" of the number of A-C passes at Higher may also have pushed teachers into over-optimistic predictions, especially as students have the fallback of compensatory A passes at the level below if they fail narrowly.
Across post-16 exams, markers told the authority of students sitting exams for which they were ill-suited, a feature which the SQA believes could be eased by more exemplification of standards and staff development in the fourth year of the new courses. The authority is considering sending staff to regional seminars.
Cathy Jamieson, Education Minister, said she had asked for a more detailed analysis involving English and maths assessment panels after pass rates fell at Higher and Advanced Higher. Reports will be published next month.
On a positive note, pass rates rose in other Higher subjects and overall pass rates at Standard grade, Intermediate 1 and Intermediate 2 had risen, Ms Jamieson said.
Anton Colella, director of qualifications at the SQA, said: "We have not diluted standards in any way. We are satisfied that the quality of papers has been in place; we are satisfied with the marking process and the conclusions of the pass mark process and we can say the standards in Scotland have been maintained in those areas."
Analysts attribute the 2.7 per cent overall fall in Higher pass rates largely to fluctuations in English and maths, which account for almost one in three of all entries. This was the first time almost all English candidates sat the new exam which has caused deep unhappiness among teachers.
English entries were up overall at Higher by 79 per cent but pass rates down by 7.6 per cent. It is suggested last year was a particularly good year - 72.3 per cent passed against 64.7 per cent this year.
In Higher maths, 5 per cent fewer candidates sat the exam but results were down 4.7 per cent. "A greater proportion of candidates than in previous years scored very poorly and this had a detrimental effect on the pass rate. There were clearly many candidates attempting this course who had little chance of success," analysts say.
At Intermediate level, where the number of entries continued to increase, many teachers entered candidates in English and communication at Intermediate 1 when Access 3 would have been better.
Overall, girls have confirmed their dominance in exam passes, doing better in Higher English and maths and gaining more A passes.