Of the original 246 entries, 70 have pulled out - 60 from science and 10 from languages - leaving 153 studying for the science bacc and only 23 for the languages one.
A spokesman for the Scottish Qualifications Authority said the withdrawal level was "in line with what would be expected".
Ken Cunningham, general secretary of School Leaders Scotland, said the explanation might lie partly in the nature of the Scottish universities' admissions system.
Pupils made unconditional offers might be tempted to leave school during S6 to earn money to help finance their higher education, while those with conditional offers were likely to drop other areas of study to focus on gaining the grade or pass they needed for the university place they had been offered. The bacc had benefits in that the interdisciplinary project was good preparation for higher education, he said.
Although the university admissions service has granted the baccalaureate interdisciplinary project a tariff of half the points of a full Advanced Higher, university admissions officers will not give applicants with a Scottish bacc preference over others in the scramble for places because it is not available in every school.
"The bacc is not a bad idea, but it came at the wrong time", Mr Cunningham said. "It should have come as we worked our way through the delivery of Curriculum for Excellence assessment, and should then have emerged as a qualification that could have been delivered nationally and recognised for university entrance.
"At the moment, it is just an additional qualification that provides an additional experience for young people. But it is not likely to deliver greater numbers of candidates for science and modern languages."
Earlier this month, Education Secretary Michael Russell told the Scottish Parliament that the SQA was hoping to launch a third baccalaureate in August 2011. It is likely to focus on the social subjects.
Elizabeth Buie, email@example.com.