A survey, carried out for the union by TNS System 3 and published yesterday (Thursday), shows that 80 per cent of teachers who were questioned believe that morale has declined since the changes were introduced.
Some 58 per cent say that pupil indiscipline has worsened, while 54 per cent say that overall school management has deteriorated. On issues of guidance and pupil support, 49 per cent point to a decline in what secondary schools are now delivering.
Ronnie Smith, general secretary of the EIS, said that in some areas changes had been brought in two to three years ago, but in others the new structures were more recent and in a minority discussions were still being held.
"What has been lacking throughout the whole process has been a real overview by the Scottish Executive," Mr Smith said. "Today's survey clearly shows that the Scottish Executive and ministers cannot sit back any longer.
"They must intervene directly to ensure that the promoted post structure in secondary schools must lead to schools which are manageable, young people in secondary schools who are seen to be benefiting from the changes and staff in schools who have confidence that the changes will have clear advantages for the school."
But a spokeswoman for the Executive insisted: "The management structure in schools is a matter for local authorities. They are best placed to determine needs locally."
Ewan Aitken, education spokesman for the Convention of Scottish Local Authorities, said it was "a bit disconcerting" that the EIS felt it had to raise a problem about school management with policy-makers rather than employers.
"This is part of the process to which they signed up themselves," Mr Aitken said.
He also took issue with the union's concerns over inconsistency across Scotland, saying that the national agreement set out a way of working which allowed each school to develop its own structure. "Perhaps we need to provide more support to schools in that decision-making and that may be part of the 2006 review of the agreement," Mr Aitken commented.
Roy Jobson, president of the Association of Directors of Education in Scotland, said: "I couldn't work out from this survey the relationship between concerns about school discipline and the structure of posts. I think they are two separate concerns."
Mr Jobson added: "I have to question how much some of the issues are to do with structures, as opposed to management and management style. If the perception is that people feel less involved, is that to do with structure or style?"
Mr Smith said he believed the link between worsening pupil indiscipline and structures was the management of departments.
"Most secondary school systems will have a system of referrals through the principal teacher. Increasingly, what is happening is that that these super-PTs, or faculty head PTs, are being deployed more like an old assistant headteacher rather than the head of a department. Instead of things being dealt with one remove from the class teacher, it is further up the line and possibly the faculty head is not there or not available."
Mr Smith warned of problems with implementing the Executive's review of the curriculum. "Could you imagine introducing Higher Still on the back of the structures that are being introduced?" he asked.
The survey, carried out in February, elicited 3,008 responses from principal teachers, former holders of PT posts, depute headteachers and main grade teachers.
While 80 per cent say that morale is worse following structural changes, 44 per cent of these say that morale is "much worse", with some councils attracting particularly high ratings in the "much worse" category: Angus (75 per cent), Dumfries and Galloway (63 per cent), Stirling (52 per cent) and Renfrewshire (59 per cent).
Few saw any benefits for learning and teaching: 61 per cent said there was no change or even a slight improvement.