It says there have been few gains from the£250m-a-year consultant contract or Agenda for Change, which has cost up to£1.8bn each year since its introduction in 2004.
There has been "an unnecessarily rushed implementation, leading to a focus on the administrative aspects of the contract without using the levers for change", says the study.
While increasing transparency and pre-empting equal pay claims, the contracts have seen productivity drop, with the decrease in output per pound "caused almost entirely by the increase in staff wages".
The impact these contracts have had on improving staff numbers is "unclear", as much of the increase occurred before they were implemented.
Working against the policy of shifting care from acute services, the number of staff in primary care is increasing at a slower rate than in secondary care.
Job satisfaction in the acute sector has declined, the report notes, possibly because subsequent pay awards were seen as attempts to claw back some of the wage rises.
The full effects of the contracts for hospital and community staff may be seen only over longer periods of time, it says.