The attack comes after Education Secretary Michael Russell published his draft Post-16 Education (Scotland) Bill.
Contained within the bill are extensive new powers that allow ministers to set priorities for universities in return for their public funding.
These include widening participation to students from deprived areas and ensuring institutions comply with new rules on governance.
The legislation also underpins significant reform of the college sector and includes powers for ministers to hire and fire new chairs of regional boards, who will oversee the changes.
It allows the Scottish Funding Council to review the provision of courses across further and higher education.
Announcing the bill, Mr Russell said college regionalisation would deliver efficiencies of £50 million annually, improve governance and ensure courses are better aligned to employers' needs.
"This bill recognises the severe financial constraints we have in Scotland without full fiscal autonomy while also delivering in a time of severe cuts to our budget," he said.
But Professor Pete Downes, convener of Universities Scotland, stressed the importance of the autonomy of institutions.
"We want to ensure the legislation gets the nature of the complex relationship between the Scottish Government, the Scottish Funding Council and universities right," he said. "Our touchstone for this is responsible autonomy – universities should be accountable for the delivery of public benefit, within a framework of institutional autonomy.
"We need the freedom to develop effective strategies for what we teach, what we research and how we achieve impact, so that we can make the strongest possible contribution to Scotland's success."
Mary Senior, Scottish official of the UCU lecturers' union, said she had "grave concerns" about the powers in the bill to open up "all aspects of provision" to ministerial control.
"This draft bill would allow ministers to review the types of programmes of learning or courses of education provided by institutions," she said.
"This opens up the possibility of political interference in the content of courses, undermining both the institutional autonomy of universities and the academic freedom of lecturers.
"While there should be a role for the funding council to ensure subject provision across Scotland, the clauses in the draft bill go much further and are a hostage to fortune."
Liz Smith, education spokeswoman for the Scottish Conservatives said the Government was treading a "dangerous path".
"This bill will diminish the autonomy of our colleges and universities and replace it with greater powers for the Scottish Government," she said.
Liam McArthur, LibDem education spokesman, said ministerial interference over the shape and content of college courses would ring alarm bells about "a power grab that could compromise the independence of the sector".
Hugh Henry, education spokesman for the Scottish Labour Party, said the bill "raises concerns about the centralisation of power in the hands of the Cabinet Secretary".