Hundreds of courses have been scrapped at schools around the country in recent years.
Figures obtained by the Conservatives show that 289 Higher and Advanced Higher courses have been cut since 2006.
On Sunday, education secretary Fiona Hyslop faced calls to take action to reverse the trend.
Conservative education spokeswoman Liz Smith said: "It is bad enough that these cuts are happening at Advanced Higher Level but even more concerning that there appears to be reductions in Higher courses too.
"It is totally unacceptable that the career choices of many of our pupils are being compromised because they cannot choose the subjects they need."
The courses cut since 2006 include 172 at Advanced Higher and 117 at Higher and cover 25 of the 32 councils around the country. They also show that 18 schools in Scotland have cut four or more Advanced Higher courses and seven schools have cut four or more Higher courses - sometimes in more mainstream subject areas like maths and history.
Ms Smith said this comes at a time the total number of Higher exams taken by youngsters rose by 14,323 between 2006/07 and 2008/09 and Advanced Highers rose by 2,930 over the same period.
"Falling demand therefore cannot be the main factor," she added. "Recent reports suggest that some schools are finding it increasingly difficult to staff some courses and in several cases it appears that courses have been cut altogether in an attempt to save money.
"We know of parents' groups complaining about this situation and their concern is naturally shared by teachers at a time when their number has already fallen by 1,000 over the last year."
Ms Smith said this comes despite pledges by the SNP to "deliver more opportunities for Scots to succeed" and to "place science, modern languages and technology at the heart of education" in their election manifesto.
"Fiona Hyslop and the Scottish Government face a major headache over this issue especially at a time when SNP education policy has inflicted so many other pressures on schools," Ms Smith added. "We must reverse this worrying trend. I hope that more schools will work together to extend the range of courses and that state schools and independent schools will work together to give as many pupils as possible as many choices as reasonable."
'INACCURATE'
But a Scottish Government spokeswoman insisted: "These claims are simply inaccurate. The fact is that pupils are taking more Higher and Advanced Higher courses, not less. Figures from SQA show that uptake has steadily increased with 137,324 pupils studying Higher courses in this session compared to 134, 030 in 2006; and 15,504 studying Advanced Highers, compared to 15,245 in 2006."
The spokeswoman continued: "Local authorities are using different ways to increase access to Higher and Advanced Higher courses including promoting collaborative arrangements between schools and the use of new technology which provides access to a range of Higher and Advanced Higher courses.
"Supporting this is the fact that education budgets are rising in real terms with record spending on Scotland's school pupils, as recent expenditure statistics revealed. This level of investment at a time of economic uncertainty is a clear demonstration of the commitment this Government has to equip our young people with the skills they need for the future."
