The Improving School Effectiveness Project (ISEP), which has attracted Pounds 500,000 in Scottish Office funding, concludes that the value added by schools to pupils' progress is complex and subtle.
Peter Mortimore, head of the Institute of Education at the University of London, jointly directed the study with John MacBeath, head of the Quality in Education Centre at Jordanhill.
Both stressed last week, when the findings were unveiled in Edinburgh, that the study underlines the dangers of making simplistic and crude judgments about "good" and "bad" schools.
"Naming and shaming doesn't work," Professor Mortimore said. "The policy-makers must learn to trust the professionals, which is just as important as establishing trust between pupils and teachers in developing the effective school."
Professor MacBeath said: "This research shows that school effects are marked by ebbs and flows, gains and losses."
The study, which Professor Mortimore said had not been attempted in any other country, conducted detailed investigations into what makes schools tick. It was based on surveys and interviews with 7,100 pupils in 80 primary and secondary schools, 2,540 teachers and 5,400 parents.
It tracked the effects of schools by checking attainment in maths and English in primary 4 and secondary 2 in 1995, and following up progress two years later. The S4 group in 1997 also included pupils' average scores from their seven best Standard grade results.
The project reports: "The pattern of adding value across the curriculum is mixed with a very few schools doing consistently well. Between 25 per cent and 33 per cent of all schools perform significantly well in one outcome and poorly in others."
A quarter of primary and secondary schools added value in maths, with a smaller proportion doing well for their pupils in English reading. Pupil backgrounds have more influence over performance in reading than in maths.
The research also found that 25 per cent of schools were doing less well than expected in maths. In English reading, 20 per cent of secondaries and 7 per cent of primaries performed "significantly below expectation".
Professor MacBeath believes such findings on "differential achievement" are among the most significant of the ISEP project.
These internal variations suggest that schools which are below par "may have an unrealised capacity to raise their performance", the projects report states. There also appears to be "scope for greater consistency of standards within the school".