Classroom discipline has been hit by a changes in how schools are run, the largest teaching union has said.
Morale has deteriorated, according to some staff
Middle-management posts have been scrapped in many Scottish schools to streamline the hierarchy.
This has been done largely by putting one senior teacher in charge of several departments.
In a survey, teachers said they thought discipline and support for vulnerable pupils had suffered. The EIS wants ministers to re-examine the changes.
Half of those who responded said overall management and guidance for children with problems had worsened, while eight out of 10 said morale had gone downhill.
Research suggested the move to merge school departments to create faculties had been patchy across the country.
Union general secretary Ronnie Smith said a "national overview" had been lacking and demanded that ministers and local authorities re-examine the changes.
"Not all council areas are going about the changes in the same way. There is no consistency either across council areas or, in many cases, even within council areas in the extent to which changes have been implemented," he added.
Mr Smith, who accused councils of failing to persuade teachers that the overhaul was workable, went on: "The survey clearly shows that the Scottish Executive and ministers cannot sit back any longer.
"They must intervene directly to ensure staff have confidence that the changes will have clear advantages for the school.
"It is this lack of confidence among teachers that the changes will bring positive benefits which is so signally lacking at the moment."
Local authority management
An executive spokeswoman said local councils were responsible for how schools were managed.
"Local authorities are best placed to know what their local needs are," she continued.
"Although changes are for councils to decide, we do keep in touch with them to find out what their experience is and we know there are examplse where it looks like restructuring is going to bring about improvements," the spokeswoman added.