Plans to reform the governance of Scotland's enterprise and skills agencies were drawn up without evidence to support them, the Scottish Conservatives have said.
Tory MSP Liz Smith said ministers had been "completely carried away with theory" without thinking about the practical implications of their proposals.
The first phase of a review of the agencies recommended last year that a new single board should be set up to co-ordinate the work of Scottish Enterprise, Highlands and Islands Enterprise (HIE), Skills Development Scotland and the Scottish Funding Council (SFC).
Opposition parties criticised the move, defeating ministers in a vote at Holyrood after uniting behind calls for HIE's board not to be abolished.
The Tories used their debating time in the chamber on Wednesday to spotlight their concerns on the implications for SFC, which is responsible for funding Scotland's colleges and universities.
Phase two of the review recommends the current agency boards should be retained ''based on more focused delivery boards around the agencies to ensure ministerial aims are delivered while also ensuring good governance standards are maintained''.
Ms Smith said the recommendation raised questions over changes to the boards' functions.
"In what respect will the powers that they have differ, or more likely be reduced, from the powers of the existing boards?" she asked.
"Specifically in respect to the SFC, will the board still be a statutory and legal entity, will it have the powers to be sources of initiative and advice, will it be able to challenge the Scottish Government in the same way it does now, and also challenge colleges and universities?"
"Will it be Parliament and not the new strategic board that would have powers to allocate resources to the agencies, and will the SFC continue to have functions way beyond enterprise and skills, such as its research function which is so crucially important.?
"It is not at all clear why in order to have better strategic alignment you need to unpick the governance structures of all four agencies.
"There was a complete absence of evidence from phase one which supports the Scottish Government's intention and now there is real concern about where on earth the Scottish Government is going."
Scottish Labour has also expressed concerns about the SFC board's future, and the impact on the autonomy of further and higher education institutions.
Labour MSP Daniel Johnson said: "The plans from the Scottish Government to create a super board threaten to be unworkable, are certainly unclear and certainly threaten the independence of our universities."
Shirley-Anne Somerville, Minister for Further Education, Higher Education and Science, said: "We will maintain a national strategic body which allocates funding independently of ministers to our colleges and universities and for research.
"This reform... can help put Scotland among the top performing OECD (Organisation for Economic Co-operation and Development) nations and I will work with MSPs from across the chamber and stakeholders beyond to achieve that goal."
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