The Scottish Government has been accused of trying to interfere in the governance of universities.
The suggestion was made by Conservatives and Liberal Democrats as MSPs began to vote on the final shape of the Post-16 Education (Scotland) Bill.
SNP ministers hope this will reform further and higher education, widen access, regionalise colleges, change governance and put a cap on university tuition fees. It is expected to pass its final stage today.
Opening exchanges exposed opposition to the Scottish Government's approach on governance, which aims to allow ministers to impose conditions when providing funding.
Tory MSP Liz Smith said: "One reason this Bill has been fraught with so many difficulties is the sharp division of opinion about this issue between the Scottish Government and the college and university sectors. They have seen the balance shift too much to the Government and from their own sectors."
Further education institutions need independence to innovate, she said.
LibDem MSP Liam McArthur said: "I remain sceptical of the need for statutory underpinning for a code of good governance for our universities.
"I'm still of the view that this encroaches into the responsible autonomy of those institutions, which is a defining feature of the best universities worldwide."
Education Secretary Michael Russell said he sympathised but did not formally support any change to the Bill.
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