Pupils are being short changed when they are taught together for different qualifications, according to a teachers union.
The SSTA wants to curb the practice of so-called "multi course teaching" in the senior years of secondary school.
It can mean students doing National 4s and 5s are being taught alongside others doing their Highers.
The Scottish government recently announced a review which will look into this.
Multi-course teaching is becoming increasingly widespread, according to the union.
The SSTA surveyed its members on the issue - more than 1,200 responded.
The survey suggested many members oppose the practice and it is much more widespread in some council areas than others.
Seamus Searson, SSTA general secretary said: "This survey has highlighted the wide variance of practice that teachers are expected to work within despite concerns raised by teachers over a number of years. The practice of multi-course teaching has wrongly become the norm in most schools in Scotland.
"It is concerning that in a time when the focus is meeting the needs for all pupils that only a minority of pupils are finding themselves in a class with all their peers following the same course.
"The high number of classes with two or three courses being accommodated in a class in S4 should be a major concern for all. "
How the lessons work
The practice stems from the way S4, S5 and S6 are now bundled together as "the senior phase" in secondary schools. The emphasis is on what qualifications the learner has achieved by the time they leave school - not what they have gained by a particular point.
The years are timetabled together - some S5 and S6 students will be studying for National 4s and 5s rather than Highers and Advanced Highers while occasionally S4 students are working towards Highers.
The practice is sometimes controversial although some within education would defend it in particular circumstances - especially in small schools or classes and in less popular subjects where separate National 4, National 5 and Higher classes may not be viable.
It might also, for example, work well when there is a degree of overlap between the different courses - for instance if the National 4 and 5 courses involves the same topics or if all the students start out on the National 5 course but some move to National 4 as the year goes on.
But it can prove more problematic in other circumstances and the SSTA would like to see an increase in the number of dedicated classes for particular courses.
They say multi-course teaching means the teacher may have to teach a range of different topics to students of differing levels of experience and ability.
What the teachers say
The SSTA published a range of comments from teachers who took part in its survey. Teachers said:
"Teaching three different courses in one class is incredibly difficult but unfortunately in our authority it is now being seen as the 'norm'. I am finding it very difficult to cope with this at times and feel that I am not doing my job the best I can. The pupils are not getting the attention they need as I am feeling stretched; at times to breaking point".
"With N4 and N5 in a single class is a complete destruction of the subject. Duplication and stupid nonsensical splitting of outcomes. If the N4 and N5 were in the same class over two years then all pupils in class would achieve the exam as pupils did in standard grade".
"The system makes a mockery of subject knowledge and has destroyed pupils' ability to succeed if they are not a high flyer. Work load for staff is ridiculous".
What the government says
The issue was raised earlier this month in a report into the senior phase and subject choices by Holyrood's education and skills committee. It said multi-course teaching should never be done on economic grounds or where it was to the detriment of the students.
A spokesman for the Scottish government said: "Multi-level teaching has long been part of Scottish education and teachers are well-skilled to take account of the needs of their pupils. There will be varying levels of prior attainment in any class.
"During inspections, Education Scotland inspectors will evaluate the extent to which children and young people are being suitably supported and challenged in their learning.
"The most important thing is the outcome for the young person - and last year a record proportion of pupils went on to positive destinations such as work, training or further study.
"Our review of the senior phase will help us to better understand how the curriculum is being implemented in schools and identify any areas for improvement."