Education Secretary Mike Russell wants to see more females on the governing bodies of higher education institutions.
He is also calling on colleges and universities to do more for gender equality, stating that too many courses are dominated by either men or women.
Mr Russell made the plea in a letter to Professor Alice Brown, the chair of the Scottish Funding Council (SFC), which funds colleges and universities.
In his letter of guidance for 2015-16, the Education Secretary said he expected universities to get just over £1.06 billion for the year, while colleges should receive just over £525 million.
A further £36 million is likely to be set aside in the budget for capital funding for colleges and universities.
But Mr Russell said while he was increasing funding, he expected the sector to continue to make efficiency savings.
He told Professor Brown: "I expect to grant £525.7 million of college programme funding, £1,062.5 million of university programme funding and £36 million of college and university capital funding in 2015-16. These indicative figures will be finalised in due course in the 2015-16 Budget.
"And while I have increased funding for both colleges and universities for the next financial year, I expect you to continue efforts to find efficiencies - specifically, and as indicated in last year's letter for 2014-15, it remains essential that the SFC works with the university sector to ensure a minimum 1% real terms efficiency saving in 2015-16."
He outlined two "strategic objectives" the SFC should consider when making funds available, with one of these being action to improve the representation of women in senior positions and to improve gender balances on courses.
In addition Mr Russell told the SFC an "immediate priority" should be how it could play its role in meeting challenges set out by the Commission on Developing Scotland's Young Workforce, which was let by Sir Ian Wood
That report "calls for an education system that is better integrated across schools, colleges, and workplaces, and which offers choices that allow young people fully to realise their potential, contributing to Scotland's economic growth", Mr Russell said.
He also pressed the SFC to encourage action from both colleges and universities that "addresses the under-representation of women on the governing bodies of colleges and universities, at senior levels and gender balance among student intakes for some key subjects".
With the independence referendum approaching, Mr Russell said he expected the SFC to play a "key role" in securing continuity of funding for research if there is a Yes vote in September.
"Independence would also provide new opportunities to extend Scotland's global reach and I would wish SFC to be proactive in establishing new relationships within these islands and overseas, seeking to further enhance the international excellence and reputation of our higher education and further education systems," he said
Mr Russell said a "good start" had been made in addressing issues raised in the Wood Report, which he said would "build on the existing links between our schools, colleges and universities to create a more integrated education system that properly recognises that there are many routes through learning and training into a career".
He added: "I have also reiterated the importance of universities and colleges leading from the front in having more women represented on their governing boards.
"Having a wider range of experience and expertise on boards will help work towards a greater equality in courses that still tend to be dominated by one gender. Institutions will look at new ways to further improve widening access, retention levels and linking to employers."
The Education Secretary continued: "A strong and effective higher and further education sector, delivering social and economic benefit for Scotland, is a key overarching objective for this government. Our regional colleges are already showing the benefits of better partnership and we have more universities in the top 200 in the world per head of population than any other country.
"Our reforms to the sector have seen the Office of National Statistics (ONS) reveal Scots to be the best educated in Europe and the Higher Education Statistics Agency (HESA) declare Scottish graduates to have the best prospects in the UK. It is imperative that we keep this momentum and commitment going to ensure the best opportunities for generations to come.
"I believe that independence will provide new opportunities to enhance the reputation of our Further and Higher education systems and extend Scotland's global reach yet further."