The Commission on School Reform has urged Scottish schools to abandon what it called the "bog standard" model of comprehensive education.
It has drawn attention to what it said was a culture of complacency in many schools.
The commission has blamed government and inspectors for their approach to schools.
Education Secretary Mike Russell has responded that schools are already benefiting from new freedoms.
Ross Martin, an adviser to the commission, said: "The key aspect for the commission is to identify where innovation is already happening.
"(We sought) to identify where we've moved away from that old template mentality of the bog standard comprehensive.
"If you look where local people are taking control, where professionals are taking control and pushing the boundaries."
But much of the criticism has been rejected by Mike Russell, the education secretary.
He said: "I don't think we have bog standard schools in Scotland.
"We have some schools that aren't performing as well as they should and aren't ambitious enough.
"But Curriculum for Excellence has made an enormous difference to Scotland's schools and we have very good teachers, very good head teachers, very good schools that are delivering lots of different things."