Nationally, there was a slight increase - to 182 compared with 174 in 2011.
Figures released this week by the Scottish Council of Independent Schools showed that 15 pupils from the sector took the qualification in 2011 compared with seven last session.
Simon Pengelley, head of Morrison's Academy in Crieff, told TESS that although it had entered pupils for the qualification in 2011, there had been no uptake in the 2011-12 academic year.
"It is not that any members of staff have been dissuading pupils, but there is a perception out there that you don't gain any advantage from doing the bacc in terms of university entrance and it could be argued that it makes it slightly more difficult," he said.
With university entrance becoming more competitive, pupils wanted to focus on getting the best grades possible and were concerned that the additional work involved in the baccalaureate and interdisciplinary project might distract from that, said Mr Pengelley.
David Knapman, head of Dollar Academy, said five of his pupils had done the science baccalaureate last session compared with four in science and three in languages in 2011.
"We think the qualification is good preparation for university work. Even though universities do not make conditional offers based on Scottish baccalaureate results, it can be a useful addition to the applicant's personal statement and we are aware of candidates who have been able to talk very successfully about their interdisciplinary project at interview," he added.
This year, schools can enter pupils for two new baccalaureates - in expressive arts and social subjects.