The issue emerged after a subject-by-subject comparison of schools' performances against national statistics. At Standard grade, Fife has comparatively few pupils getting the two top grades in English and maths. In maths, the trend over the years is downwards.
In Higher English, the pattern is repeated with figures slightly below the national average. Maths again raises concern with low numbers of presentations and relatively little success in band A passes.
Low numbers in Standard grade technology and creative and aesthetic subjects raise the question whether Fife schools are implementing guidelines on balance in the curriculum, the study suggests.
But performance in Standard grade modern studies is "exceptional" and cannot be explained by the relatively high number of pupils taking the subject. Accounting and finance is another strong area. More pupils do general science than elsewhere in the country and correspondingly there are fewer presentations in physics, chemistry and biology, a situation the education department wants to study further.
Higher languages give contradictory messages. French is on a decline, but German is relatively strong and Latin "very sound".
Alec Thomson, chair of education, said that Fife was "an open council which wants to show people the true picture, both good and bad". Pupils were well served but there was always scope for improvement. "Attainment in education is adversely affected by difficulties with poverty and unemployment, something which Fife has more than its fair share of," Mr Thomson said.
The study found little of significance in the Scottish Office's use of relative ratings. At Standard grade only one subject, classical studies, had been singled out for its low rating, but Higher results in the area were good.