Statistics on the make-up of the boards running universities and colleges show that on average fewer than one-third of members are women.
Men also dominate the senior management teams of Scottish universities, although the picture is better in the college sector, where approaching half in management are women.
Scottish Labour's equalities spokeswoman Jackie Baillie, whose team gathered the figures, said they showed a glass ceiling was still in place in higher and further education.
Yesterday The Herald revealed the extent of the gender imbalance at the very top of Scottish public bodies, in areas such as arts and culture, tourism, justice and health.
Overall, figures gathered under freedom of information requests by Ms Baillie's team show 570 women are among 1784 board members identified as running Scottish public life. This equates to 33.02%.
However, the statistics for higher and further education are even poorer. On average, board membership at universities is only 31% female, and in colleges the figure is 30%.
Senior management teams in universities are 36% female, while in colleges the figure is 46%.
Universities with particularly low levels of involvement for women on their boards include Heriot-Watt (10%), Strathclyde (13%), the University of the West of Scotland (17%) and Aberdeen (21%).
In the college sector, Anniesland College reported 15% of board members are women and at Coatbridge College it is 19%.
In February, The Herald revealed figures showing university ruling courts were just 25% female - despite the fact women academics make up more than half the workforce. Education Secretary Michael Russell described that statistic as "stark and alarming".
Jackie Baillie, Scottish Labour's equalities spokeswoman, said the Scottish Government had missed a chance to make gender quotas mandatory as part of its post-16 education bill. She said: "This was a missed opportunity that has the potential to impact current and future female students on a variety of courses. It's clear we still have a long way to go to shatter the glass ceiling.
"I urge the Scottish Government to face the reality that many women who are skilled and highly trained are unable to break the culture that holds that glass ceiling above their heads and that they can take positive action to stop that happening."
Ms Baillie has called for quotas to address the gender imbalance her FoI requests have identified.
Universities Scotland director Alastair Sim said a new governance code for universities includes goals for increasing the diversity of governing body membership, and argued this was a better approach than imposing quotas on the sector.
He added: "University governing bodies include staff and student members who are elected by their peers, on the basis of their electorates' choices about who is the best individual for the role regardless of gender.
"For this and other reasons we do not think rigid gender quotas are the right way of securing diverse membership of governing bodies in a way which commands the confidence of the university community."
John Henderson, chief executive of Colleges Scotland, said: "The college sector in Scotland has a strong record of appointing female principals and the representation of women on senior management teams, is 46%."
He said reform of the sector offered opportunities to tackle the problem. "As a sector, we are ambitious about encouraging equality. This is a good time to improve the representation of women on college boards following regionalisation," he added.
As part of ongoing reforms to the college sector, the Scottish Government is currently recruiting 12 college chairs and board chairs through the public appointments process.