Official figures show entries have slipped about 10% this year after the introduction of National exams, which replace Standard Grades.
The Scottish Qualifications Authority (SQA) says pupils will take an average of 6.8 Nationals this summer, against the 7.3 Standard Grades sat last year, fuelling concerns among educationalists that subject choices for young people are being restricted.
It is understood enrolments for language exams are down more than 10%, while the decline in sciences is about 8%. Maths and English enrolments have remained stable.
Larry Flanagan, general secretary of the Educational Institute Of Scotland, the teachers' union, said: "There is some evidence certain subjects are being squeezed out. One school told me history was being removed in the S1-S3 curriculum, which beggars belief.
"There was never any intention to marginalise subjects and if that is happening then that is an error."
However, the Scottish Government said the new curriculum allowed for pupils to sit exams at different times and that total qualifications achieved by school-leavers was a more important measure of achievement.
The new qualifications were introduced as part of the Curriculum for Excellence reforms, which were intended to provide a broader education for pupils.
But whereas Standard Grades were studied over two years from S3 to S4, the new exam courses of 160 hours are being taken over one year in S4. That leaves some schools with too few teaching hours to fit in more than six subjects.
Brian Boyd, emeritus professor of education at Strathclyde University, Glasgow, said the trend was worrying.
He said: "If the average is dropping to below seven qualifications then we should be asking serious questions because it would seem to me to be a narrowing of choice.
"There is no good reason why pupils should do fewer than seven subjects and if that is a by-product of the new curriculum it has to be looked at."
Alan McKenzie, acting general secretary of the Scottish Secondary Teachers' Association, said Curriculum for Excellence had originally envisaged schools doing as many as eight subjects.
"Young people must be given the fullest choice of qualifications to study and it is always worrying when they are not getting it," he said.
A spokeswoman for the Scottish Parent Teacher Council added: "There continues to be some anxiety from parents in relation to the number of Nationals being offered. In some cases parents feel the range is not sufficient and that this will limit their child's options at Higher.
"Where parents are simply told of a decision once it has been made, there can be no surprise when they are frustrated or angry about what is being done."
However, the Scottish Government, the SQA and curriculum body Education Scotland argued pupils would still experience a broad education, would sit further qualifications in future years and have more time for in-depth learning.
It was also stressed schools could use new flexibility over timetabling for brighter pupils to study greater numbers of Highers by skipping Nationals altogether.
Minister for Learning Dr Alasdair Allan said: "Some schools are doing six or seven exams in fourth year, but the reason behind that is not to narrow choice. It is to increase depth of understanding and allow pupils to come out of school with more qualifications by picking up more subjects in fifth and sixth year."
Graeme Logan, strategic director with Education Scotland, said: "As this reform takes place, it is inevitable there will be changes in patterns of presentations for qualifications.
"Decisions on the pattern and number of subjects should be based on maximising achievement and qualifications by the time young people leave school. For some, this might be fewer subjects in S4, but leading to a higher levels of qualifications overall."
Dr Gill Stewart, SQA director of qualifications, said the new Nationals were designed to better recognise the achievement of young people across the whole school year and to ensure they demonstrated both knowledge and understanding of a subject, as well as wider skills of analysis and interpretation.
The SQA figures show that in January the total number of entries at National 4 for pupils in S4 was 97,000, with 230,000 enrolments at National 5.