The call came after figures show the number of pupils sitting Scottish Baccalaureate exams fell eight per cent in 2014 - from 191 to 176.
The Scottish Government introduced the baccalaureates in 2009, claiming they would develop deeper learning and critical thinking skills, as well as promoting important subjects.
Originally developed in languages and sciences, the initiative was expanded in 2012 to include two new baccalaureates in expressive arts and social sciences.
However, figures from the Scottish Qualifications Authority (SQA) show only three pupils sat a baccalaureate in expressive arts this year, compared to five in 2013, while there were only 15 entries for the social sciences qualification.
The number of pupils taking a language baccalaureate fell from 32 to 22 over the same period and there was also a drop in those studying the science qualification, from 142 to 136.
Alan McKenzie, acting general secretary of the Scottish Secondary Teachers' Association, said schools had always been unsure of the merit of the qualifications.
He said: "We are now of the view it is time to scrap them because they are an added complication in a system that already has high quality alternatives in the form of Advanced Highers.
"There was always a suspicion these were politically motivated qualifications introduced by the Scottish Government to make them look better than the opposition, but schools were never convinced. The qualifications are not seen as being worth the effort and we should be concentrating on Highers and Advanced Highers, which are the gold standards of the system."
Larry Flanagan, general secretary of the Educational Institute of Scotland teaching union, added: "Schools have been swamped with changes to the qualifications system and teachers do not have enough time to run with the new range of options. If someone is doing the baccalaureate project it needs to be supervised and there is not the time to do that given the current workload.
"The principle of these qualifications is fine, but it is not a school-driven initiative and, with the upgrading of Advanced Highers to ensure they provide a good preparation for university, it is difficult to see it becoming a priority for most schools."
A Scottish Government spokeswoman said it would ask officials from the country's exam body to assess the decline.
She said: "It was always expected Scottish Baccalaureates would be studied by a small number of our brightest pupils in S6.
"We will, however, ask SQA to examine the drop in entries this year and provide further support and advice to schools where necessary."
Developed by the SQA, the qualifications were aimed at high-achieving sixth-year pupils. They consist of a group of related Highers and Advanced Highers, as well as an interdisciplinary project chosen by the student and marked to Advanced Higher level.
After initial interest the qualifications were seen as time-consuming, with a relatively low rating from the Universities and Colleges Admissions Service (Ucas), which oversees university entry.
Ucas currently scores the interdisciplinary project at 65 tariff points for an A grade, whereas pupils can gain 72 points for a D grade at Advanced Higher and 130 points for an A grade.