Glasgow, the largest council, is moving towards new faculty structures that will see the demise of subject PTs and their replacement by far fewer curriculum PTs. The first dozen umbrella curriculum posts were filled before the summer break and others will follow.
George Gardner, depute director of education, said it was "not something we can do overnight" because of the age profile of senior staff and cost.
However, the authority would fill vacancies as they arose with curriculum managers.
There are around 550 subject PTs and another 200 guidance or pastoral care PTs in Glasgow. Instead of 15-18 subject PTs in secondaries, numbers would fall to eight to 10, depending on the size of school, Mr Gardner forecast.
The city's commitment to eliminating vast tranches of middle managers has angered the Scottish Secondary Teachers' Association, which has accused the council of "cash saving". It warns authorities to expect a backlash from experienced teachers who will no longer want to take on extra duties.
Jim Docherty, SSTA assistant secretary, said: "I have no idea of the extent to which elected representatives understand the problems they are creating for themselves."
Only subject PTs with a background and knowledge of their specific area could respond to national documents, implement strategies in their subject and liaise with the Scottish Qualifications Authority on exam details, he said.
Mr Docherty added: "There will be a significant number of areas where no one will do the job. Job-sizing aspects will have to be taken into account, and what will the salaries be? They could be pound;3,000-pound;4,000 more or nil more. Our policy is that each individual subject should be dealt with on a departmental basis and headed by a PT qualified in that subject."
He is further alarmed at Glasgow's plans to create project leaders with the veiled threat that ambitious teachers are unlikely to become PTs without first taking on extra responsibilities.
Mr Gardner said schools had been consulted on the changes and were now trying to ensure groups of subjects had "coherence".
"For example, a school may have scientific studies or social studies and to some extent these are already in place. It might also have a PT performing arts which could include drama, music, physical education and maybe art.
Clearly, there would be variations that would emerge in a small secondary school. You might have a PT language and communication which would include English and modern languages," he said.
In Inverclyde, says the Teachers' Agreement Communications Team, secondaries are being urged to retain principal teachers in core areas such as English and maths.