Ewan Aitken, education spokesperson for the Convention of Scottish Local Authorities, said the report confirmed that the agreement had brought benefits to everyone.
"Teachers have had increased salaries and the support they asked for, including CPD and help from non-teaching staff," Mr Aitken said. "Pupils have also had more support than ever before. And the bringing together of employers, teachers and the Scottish Executive in negotiations has brought stability to schools and less of the old conflict politics."
Mr Aitken said that Audit Scotland was essentially saying: "You have made the progress expected of you, given the complexity of the issues." It was asking the questions that he would expect.
He said the report's concerns at the lack of performance measures were understandable but added: "What we had here was a process in which it was understood that a cultural change was required in schools. We couldn't wrap that up in numbers; it's more complex than that."
Mr Aitken said there was an added difficulty in quantifying costs and benefits at a time when headteachers were being given more flexibility and control over combined budgets.