The Royal Society of Edinburgh (RSE), Scotland's national academy of science and letters, said the proposed Post-16 Education (Scotland) Bill ignored the "fundamental right" of universities to be autonomous. It is the latest criticism of the Bill, unveiled by Michael Russell, the Education Secretary, last year.
Last week, Alan Simpson, who leads the body that represents the chairs of university courts, said the legislation would pave the way for the greatest political influence over higher education for more than a century.
And this week the principals of four universities warned the Bill risks undermining the ability of the sector to compete on the global stage.
The legislation is controversial because it lets ministers set priorities for universities in return for public funding – including ensuring institutions comply with new rules on gover-nance and widening access.
It also gives the Scottish Funding Council (SFC), which administers public money on behalf of the Government, powers to review the provision of courses.
A written submission from the RSE to the Scottish Parliament's education committee – which is scrutinising the legislation – said the Bill went too far.
The submission said there was an absence of an "overarching strategy" and called the proposed changes "ad hoc".
It stated: "The Bill provides Scottish ministers with significant powers to determine principles of governance or management in relation to universities.
"Oversight of management effectiveness is one of the principal functions of each institution's governing body and we see no justification for its inclusion in the present Bill.
"The fundamental right and need for universities to enjoy autonomy in their strategies and operations is not being sufficiently recognised."
The RSE was equally scathing about the potential implications of proposals for the SFC to review course provision.
It said: "It is the institutions themselves that are best placed to determine such matters, depending upon their individual circumstances."
While the RSE said it strongly supported measures to widen access, it "remained to be convinced" a ministerial requirement on the issue would improve the situation.
The submission concluded: "Fundamental questions remain as to why a review of higher education governance was initiated and what public concern was it designed to address.
"There has been no explanation of how the proposed changes will improve the existing arrangements for governance and we are concerned that the proposals are in danger of putting at risk the significant gains which have been made."
Universities Scotland, which represents university principals, also attacked the proposals in its written submission on the Bill.
It said: "We do not see a need for the higher education provisions in the Bill, which create new, and quite extensive and unspecific powers over higher education institutions.
"While universities are keen to continue to work with the SFC to widen access - the Bill gives the impression there is a problem which needs to be addressed through legislation, which in our view is not necessary."
A Scottish Government spokesman said: "The Government is listening to all points of view during this process of pre-legislative scrutiny."