Credit is given to schools that have used curriculum flexibility to improve the quality of learning for a number of pupils, notably the lower-attaining.
But the report points out that, given the aims set out in A Curriculum for Excellence, secondary schools need to look again at how they do things.
Key strengths of the secondary sector are said to include strong pupil performance by international standards, a high level of pastoral care and postive ethos in many schools, teacher skills and commitment, and the particularly positive impact of many headteachers on the community life of their school.
However, the report calls for improvements, particularly in "engaging, challenging and motivating all young people", bringing greater consistency to the quality of learning experiences and developing leadership so there is a stronger drive on improving learning and teaching.
Inspectors report that the proportion of schools in which the overall quality of attainment at S1-S4 is fair or unsatisfactory remains too high, although the picture at S5-S6 is more positive.
They recommend the use of ongoing assessment to improve the quality of learning and add that, too often, ICT resources are not used effectively, even when they are readily available.
The report also refers to the decision by some secondaries to use the relaxation in age and stage regulations to change pupils' curricula and the stage at which they take national qualifications.
"In a number of cases, changes are well considered and appropriately monitored and evaluated, and lead to increased motivation. At times, however, changes are introduced without adequate preparation or sufficient consideration of the potential effects on pupils' learning and future opportunities.
"In addition, schools have sometimes sought to provide alternative experiences or programmes without sufficiently considering how pupils'
current experiences and programmes could be improved. Educational gain for pupils as a result of curriculum changes is, in a considerable number of cases, as yet unclear."
Senior managers in the most effective schools have a shared leadership culture which views improvement as the responsibility of all staff.
However, in a significant minority of schools the quality of leadership was found to have important or major weaknesses.
This produces knock-on weaknesses in aspects of school ethos, poor teamwork, a lack of shared responsibility and accountability, and limited improvement in pupils' attainment and achievement, HMIE says.