The university sector has expressed widespread anxiety about provisions in the Post-16 Education Bill that would allow ministers to impose conditions on universities to adhere to "good practice in governance".
The heads of four Scottish higher education institutions appeared before Holyrood's Education and Culture Committee today to outline their concerns.
University of Edinburgh principal Sir Timothy O'Shea said: "We have a principle anxiety about the legislation.
"We are very supportive of the whole Bill in terms of intentions with regards to widening participation, greater efficiency of the sector and greater accountability.
"At the same time, we are very aware that the Scottish universities are seen as being particularly successful, and the outside commentators relate that success to the responsible autonomy that we discharge."
He added: "We are anxious that there may inadvertently be a potential reduction in responsible autonomy and that some future administration might be in a position to intervene in a way that would be unhelpful to the success of universities."
He continued: "Our experience since devolution has been that we have, with the four governments, had a very constructive engagement and we have flourished in comparison to other European and English education systems.
"Our anxiety is that if a future government were given the apparatus whereby it could intervene in our management or governance structures then it might choose to do so.
"And clearly if you look around Europe you find examples of countries where governments, or regional governments, do intervene in the governance of universities and it is clearly unhelpful."
Glasgow School of Art director Seona Reid said: "The issue of a code of governance is something that all universities, or whatever size or nature, supports absolutely wholeheartedly.
"But to enshrine it in legislation risks the possibility that for future administrations it could be misused to apply a uniformity of governance model that would be inappropriate to a diverse sector."
Committee convener Stewart Maxwell quoted Tracey Slaven, from the Government's Bill team, who told the committee last week that they are listening to the sector's concerns about "unintended consequences" of the Bill.
Mr Maxwell said: "It sounds like they are certainly reconsidering their position. Is that your understanding?"
Sir Timothy said: "I met with Tracey Slaven yesterday and that was my exact understanding."
Labour learning and skills spokesman Neil Findlay challenged the universities` concerns, suggesting that conditions may have to be imposed to address the shortcomings of institutions that have "failed miserably" to widen access to their courses.
He cited Aberdeen University, which has 2.2% of students from deprived backgrounds, and St Andrews University, which has 2.6%.
"I would suggest part of the reason why the Government is seeking to legislate is because of the approach that you are presenting to us today," he said.
"They feel that things haven't gone far enough, therefore they feel as though they are going to have to legislate."
The panel unanimously disagreed with Mr Findlay's analysis, insisting that the figures do not tell the whole story and that access has improved.
Ms Reid said: "There has actually, over the last six years, been a 16% increase in (deprived) university students.
"That's 3,053 students from those postcodes, so the figures are misleading in the terms that they are being presented."
In a statement released after the committee, Conservative education spokeswoman Liz Smith said: "Scotland's higher education institutions have a distinguished reputation and it is very clear from the evidence we heard today that the primary reason for this success is the responsible autonomy under which they have operated over a long period of time.
"They are right to be very concerned about the proposals within the bill to substantially increase the powers of ministers which, by definition, would undermine the autonomy which has made them so successfully competitive and so admired around the world.
"There is a wide range of statistics that show very clearly that those higher education sectors around the world which achieve the highest level of success in academic, economic and social terms, are those with the greatest degree of autonomy.
"Indeed, there are many countries around the world which want to further remove the involvement of the state in universities.
"So why is the Scottish Government doing the reverse?
"That is a stark message for the SNP and it is little wonder why the university sector at large is questioning the need to legislate for more ministerial power."