Ministers' emphasis on business involvement in education action zones ensured that they started work in an atmosphere of hostility and suspicion with many teachers fearing their schools would be privatised, it found.
As a result of the tensions, zone directors and education authorities had to spend time and effort persuading schools that they had no reason to fear joining a zone.
The research, commissioned by the National Union of Teachers, found early zones were forced to begin more cautiously than they would have liked. Chris Kirk, a consultant for PricewaterhouseCoopers, said this had scuppered ministers' plans for them to be testbeds for educational experiments in the inner cities.
No zones had taken advantage of regulations which would have allowed them to disapply teachers' national pay and conditions or to cede their schools' powers to forums dominated by private firms, said Mr Kirk, who previously worked for the Deparment for Education and Employment on the initiative.
Doug McAvoy, NUT general secretary, said: "In education action zones, the Government created potential for teacher-led innovation. But through its ferocious spin on a lead role for business, it guaranteed a lack of confidence in the model it was proposing."
Data from the DFEE showed that educational standards rose quicker than the average in zones, but it was difficult to attribute this to an "EAZ effect" rather than to extra funding or other initiatives such as literacy and numeracy strategies, the PricewaterhouseCoopers report argues.
Teachers were divided on whether being part of a zone raised standards - more than half agreed it did while 40 per cent did not believe improvement could necessarily be attributed to the zone.
The report concluded: "A clear message for the Government is to trust teachers and others to deliver and to communicate unequivocally what it expects and why. The Government needs to think very carefully about the impact of its statements on the range of stakeholders in the process."