Parents have claimed their children's education is being affected by new rights which allow teachers time away from pupils under the McCrone deal.
A survey by the Scottish Parent Teacher Council suggests widespread concern.
Those questioned said head teachers and classroom assistants sometimes had to provide cover or children were left to watch television and videos.
Local authorities said some schools may not have explained the changes well enough to parents.
The McCrone agreement, reached in 2001, secured a 23% salary rise over three years for Scotland's 50,000 teachers.
The deal also capped teachers' working week at 35 hours and included the hiring of 3,000 more support staff.
Head teachers have been complaining for some time about a change in the working pattern of teachers introduced by the McCrone deal.
"We would be concerned if classes are being cancelled because of a lack of available teachers"
Staff are now entitled to spend up to half a day less each week in the classroom.
The free time is given over to marking and planning lessons.
Some parents have queried why this work cannot be done in the afternoon after youngsters have gone home.
However, other parents said they were happy about teachers' absence as long as the children received lessons from visiting arts, sports and science staff.
Judith Gillespie, from the SPTC, said in some schools head teachers were taking classes together in an extended assembly just to keep them occupied.
"This clearly doesn't replace lessons," she said. "It also takes head teachers away from the job they ought to be doing."
David Eaglesham from the Scottish Secondary Teachers Association (SSTA) said: "We would be concerned if classes are being cancelled because of a lack of available teachers and I think that's something local authorities and the Scottish Executive need to address."
A spokesman for the Educational Institute of Scotland, said: "Local authorities and school management teams should see the reduction in class contact time as an opportunity to enhance pupils' educational opportunities through the deployment of visiting subject specialist teachers.
"Parents obviously want the best for their children, and teachers share this aim, and the reduction in class contact time was always intended as a means of enhancing the educational experience for all pupils."
He added that it should be taken into account that the response to the survey was only 12%.
A spokesman for local government body Cosla said: "Councils are committed to improving communication and we will certainly take the SPTC's findings seriously.
"If some schools have not communicated their plans well enough, that is unfortunate and we would be happy to meet with the SPTC and see how we could address their concerns.
"It is unfortunate that the SPTC have chosen to communicate their report via the press rather than directly with local authorities or Cosla."
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