Although 47% of staff at universities in Scotland are female, only 21% have been promoted to professorships, figures compiled by The Herald reveal.
The situation has remained static since 2007, when legislation was introduced to improve gender equality.
Heriot-Watt University has the lowest proportion of female professors – just 12% of promoted staff are women – followed by Abertay, in Dundee (13%).
Glasgow Caledonian University has the highest, at 31%.
There are just five female principals out of a total of 19 Scottish higher education institutions – 26% – although that compares favourably with England, where just 12% of principals are female.
Mary Senior, Scottish official of the University and College Union, which represents lecturers, described the figures as "deeply disappointing" and called for action.
"It is quite clear there is still a glass ceiling in academia in Scotland, and we remain concerned that the career path is all too often incompatible with having children and balancing family and caring commitments," she said.
"The long-hours culture is endemic in the university sector with constant pressures to improve research outputs and publications in order to get promotion, which places those with family responsibilities at a clear disadvantage.
"We need leadership from the top to change the culture in universities."
Emma Ritch, project manager of Close the Gap, a Scottish Government-funded body which works to promote equal pay, said the figures reflected discrimination in the wider labour market.
She added: "It is of additional concern in science, technology, engineering and maths, where we see a leaky pipeline effect, with women leaving the disciplines at each level.
Kelley Temple, NUS Scotland women's officer, said it was time for universities to "face up" to the imbalance.
"Whether in the business, political or academic community, women are not being given the opportunities to succeed," she said, adding that a lack of women in senior positions meant fewer role models for students. "The Equalities Act was enacted to address just these kinds of inequalities, but clearly it's not working," Ms Temple said.
Alastair Sim, director of Universities Scotland, which represents principals, said the institutions were working hard to improve the balance.
"As employers, universities want to see equality for all staff, including gender balance at the highest level of academic posts," he said.
"Regrettably, gender balance still varies significantly across disciplines and universities have long been aware of women's low progression rates to the highest levels in the sciences, technology, engineering and maths."
Heriot-Watt said its status as a science, engineering and technology-based institution "went some way to explaining" the lower numbers of female academics, particularly professors.