John Travers, the council's director of education, in his observations on the Inspectorate's report on Achievement for All, said research did not support HMIs' preference for setting and said their case ignored the reality in schools.
Mr Travers stated: "An inflexible adherence to setting by ability in English and mathematics in S1 would place great stress on national testing, either in P7 or S1, and would lose the benefits of current methods of class construction which take account of a variety of personal, social and academic factors. "
He added: "These major reservations have given rise to criticism of the report on the grounds that it is inspired by ideology rather than by objective judgment."
Previous research on setting was inconclusive or cast doubt on the effectiveness of setting in improving attainment. In some cases, setting lowered pupil motivation and teacher expectation, thus reducing attainment.
Doubts also surround the Inspectorate's backing for whole-class teaching, the director reported. Even a class set by ability contained a wide range of ability levels and differing needs might be met by other methods. "It is notable that previous reports by HMI have praised schools for adopting flexible methodologies rather than seeking to advocate only one approach," Mr Travers noted.
Setting would have major implications for staffing, resources, timetabling, methodology and guidance in the first two years of secondary school on top of similar demands in the fifth and sixth years in preparation for Higher Still programme.