Opposition politicians branded the situation a "national disgrace" and called on ministers to rethink their priorities.
Michael Russell, the Education Secretary, has already been attacked for cutting teaching budgets for colleges by £73 million during the recession.
However, The Herald has obtained figures showing that the number of female learners has declined by more than 26% since 2006/07 – from 161,559 to 118,447 – while the number of male students has dropped by 13% – from 111,352 to 96,104.
The disproportionate decline in women learners follows the Government's decision to prioritise full-time courses for younger students to cut youth unemployment.
As a result, the number of part-time, weekend and evening courses has been reduced, with funding withdrawn for many.
A Scottish Funding Council report on the issue has highlighted how the move has had a greater impact on females.
It said: "Short full-time study is much more common among men, being commonly associated with training for trades. Evening and weekend and distance or open learning are more popular with women and more women participate in part-time day courses, although the number has declined over the five-year period."
John Henderson, chief executive of Scotland's Colleges, said: "One of the enormous strengths of the college system is its ability to cater for a diverse range of students at different times in their lives. Any narrowing of that risks limiting the opportunities available.
"These statistics indicate that fewer women are undertaking part-time courses. The SFC should carefully examine the trends ... to ensure no particular groups are being disadvantaged."
A spokesman for the Educational Institute of Scotland. the union which represents college lecturers, called on the Government to ensure equality of opportunity for all learners.
"The Scottish Government took a political decision to prioritise full-time college courses, but must also be prepared to address the consequences of this decision," he said.
"We already know the number of people studying in colleges has fallen as a result of this, and now there is emerging evidence that women have been disproportionately affected.
"Many women, particularly those with caring or childcare responsibilities, need the flexibility offered by part-time education at college to allow them to balance their working, learning and caring commitments."
Opposition politicians also went on the attack, calling the situation "shameful".
Kezia Dugdale, youth unemployment spokeswoman for Scottish Labour, said: "At a time when women are being hit the hardest by Tory-led Government cuts and worst affected by unemployment, it's a national disgrace that more than 43,000 Scottish women, twice the number of men, have simply vanished from further education."
Scottish Tory chief whip John Lamont said: "The SNP's misguided approach to college education was always going to hit those more likely to study part-time, such as women."
A Scottish Government spokesman said: "The Scottish Government is seeking to tackle inequality in gaining employment and recently hosted Scotland's first Women's Employment Summit involving the First Minister," he said.
"We are committed to maintaining full-time equivalent college student numbers at 2010/11 levels."