In an article for this week's TES Scotland, Mr Paterson claims his company is the established market leader in job-sizing and accuses its rival PricewaterhouseCoopers, which carried out the exercise, of "fundamentally poor practice" in refusing to share the principles behind its scheme with those affected by it.
The result, he says, is that the promoted staff involved do not understand what it takes to "win" under the new system or why they may have "lost out".
Mr Paterson says the exercise was flawed and calls on headteachers to be given support as a matter of priority so they can manage the motivational fallout from an exercise which has been "overly complex, poorly understood and counter-productive".
In what is the first public critique of the job-sizing exercise from within the industry, Mr Paterson takes particular issue with what he sees as an unnecessarily complex process.
"By looking at more than 30,000 teaching roles in Scotland individually and creating no fewer than 19 different levels, a degree of differentiation has been introduced which, in our experience, we simply do not believe exists or is warranted," he writes.
The Hay Group chief suggests that there are only five or six real levels of teacher, from trainees to heads. "To break this down further leads to absurd levels of differentiation, made worse by a real lack of transparency in how the system works in practice. This, in our opinion, has been a major design flaw."
Mr Paterson predicts that, unless heads are helped to understand the new system, "upward salary drift" will result. "It is not unreasonable to think that, as a headteacher faced with something you do not properly understand, you would do your best to play the system to get as many of your people up the salary bands as best you can," he writes "While this is understandable, it is hardly the intended effect of the exercise. What may emerge is creative job redesigning and restructuring."
The main parties to the teachers' agreement are continuing to insist on the benefits of the package in its entirety, including the job-sizing deal. As recently as two weeks ago, Peter Peacock, Education Minister, rejected calls at the secondary heads' conference for a review of the job-sizing toolkit. "There is no going back," Mr Peacock declared.