Nicola Sturgeon has been called on to drop a controversial Bill that would shake up the governance of universities.
Scottish Conservative leader Ruth Davidson said the plans would cause "huge harm" to the sector, damaging academic independence and the funding of institutions.
The First Minister said the Higher Education (Governance) Scotland Bill currently making its way through Holyrood was necessary to improve university governance and ensure staff, students and trade unions are represented.
Universities fear additional controls handed to ministers through the Bill could result in their reclassification as public-sector bodies, restricting their ability to borrow funds and risking their charitable status.
Speaking during First Minister's Questions at Holyrood, Ms Davidson cited independent legal advice obtained by Universities Scotland, which represents Scotland's 19 higher education institutions, that the reforms would create a "significant risk" that institutions could lose their charitable status.
She said: "Political interference, suppression of critical thought, meddling, devastating, dramatic and harmful.
"That is what academics think of the Scottish Government's Bill to increase political control over the way universities are run.
"The reputation of our universities has been founded on their academic independence, their sustainable funding depends upon their charitable status.
"This Bill at a stroke threatens to demolish both of those foundations. It is a Bill that can cause huge harm but doesn't appear to give us any gain."
Earlier this week, Professor Sir Timothy O'Shea, principal and vice-chancellor of Edinburgh University, urged MSPs to put the Bill on hold.
Ms Davidson continued: "The Bill is a mess, the universities hate it.
"They say they haven't been properly consulted on it, the legal advice says it could threaten their charitable status and it risks blowing a gaping hole in higher education funding. All for reasons that the Scottish Government struggles to explain.
"Isn't it time that the FM recognised this and she drops this damaging Bill?"
Ms Sturgeon insisted the legislation was "not about introducing ministerial control over universities" but said the government would continue to "engage constructively" with universities.
She quoted the view of the Office of the Scottish Charity Regulator that the proposals "would not affect the constitutions of higher education institutions in ways that would give ministers the power to direct or control these institutions' activities", and should therefore not impact on their charitable status.
The First Minister said: "It is about ensuring that the governance of our universities is transparent and inclusive. That's why the Bill has been welcomed by students and trade unions.
"I actually think there is very good reason and good argument to say that we want staff, teaching and non-teaching staff, and students to be properly and appropriately represented on the governance of their institutions.
"That is what this Bill is about and I think that's an important objective.
"All of us across this chamber, I know I certainly do, want to see our successful universities go on to be even more successful in the future.
"That is in the interest of the government, it is in the interest of our country as a whole and it is ridiculous to suggest that this government would do anything that would put that at risk."
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