The Scottish Government said "gender segregation" in subjects such as physics, chemistry, engineering and computer science had to be tackled.
Institutions have also been asked to create a better gender balance in courses that are largely populated by females, such as nursing, teaching and social work.
Recent figures show 65 per cent of students studying science and engineering courses in Scotland are male, while 80 per cent of those taking computer science are men. Nearly 80 per cent taking education courses are women.
In a letter setting out his priorities for higher and further education, Michael Russell, the Education Secretary, said: "I want a renewed focus on reducing gender segregation in participation. Too many college and university courses are dominated by either men or women."
A Government spokesman added: "We are determined to address gender imbalance in a number of careers as, although the picture is improving, we need more young women to be attracted to the high-value jobs available across key growth areas such as in engineering, ICT and the sciences."
Mr Russell also called for better representation of women on the governing bodies of universities, colleges and at other senior levels.
Figures published earlier this week showed just 31 per cent of the members of university ruling Courts in Scotland are female, although the figure has risen from 25 per cent last year.
Senior management teams in universities are 36 per cent female. In colleges the figure rises to 46 per cent.
Mr Russell added: "The second strategic objective is to encourage action ... with colleges and universities that addresses the under-representation of women on the governing bodies of colleges and universities."
The letter from Mr Russell - sent to the Scottish Funding Council (SFC) to set priorities for the sector - confirms overall funding of £526 million to colleges, £1,062m to universities and £36m to both sectors for capital funding in 2015/16. Universities have also been tasked with finding a minimum of one per cent efficiency savings.
Universities Scotland, which represents university principals, warned wider societal issues that dictated subject choice also had to be tackled.
Earlier this year the first female president of the Royal Society of Edinburgh, Professor Dame Jocelyn Bell Burnell, warned that girls were put off studying science at school because their families thought subjects such as physics were more suited to boys. A Universities Scotland spokesman said: "Every course at every Scottish higher education institution is equally open to both males and females and universities already look to encourage and inspire participation in courses where there has traditionally been a gender imbalance.
"While universities have an important part to play in any effective challenge to wider society's attitudes and stereotypes which might label a course or profession as belonging to one gender or another, they are just one factor and it is important the equal opportunities message is promoted at all stages of the learner journey starting from nursery."
Vonnie Sandlan, women's officer for student body NUS Scotland, said: "In too many institutions, across too many subjects, women find themselves excluded and underrepresented, particularly in the cases of science and engineering.
"If we're serious about building an economy which works for everyone, women need to be right at the heart of that, and supported in studying those subjects from which they've been missing from for too long."
The letter also calls on more action by institutions to tackle drop-out rates. On research, the minister urged the SFC to support universities less active in research but where there was "evidence of emerging excellence".