In a joint submission to MSPs examining the Further and Higher Education (Scotland) Bill, the Association of Scottish Colleges and Universities Scotland endorse the legislation as it stands.
"We firmly believe that the Bill now achieves its aims successfully without unnecessary disruption or the risk of damaging unintended consequences," they told the parliamentary enterprise and culture committee this week.
Colleges and universities were particularly exercised that the merged council would become a planning and interventionist body, leading to "unnecessary and unhelpful bureaucracy and restructuring".
The ASC and Universities Scotland told MSPs: "The funding body is situated between government and institutions. Its role should be to facilitate communication in both directions.
"The funding body funds capacity of colleges and universities to deliver teaching and research. It is not - and must not be seen as - either a purchaser-provider or an all-purpose regulator. It should act strategically and avoid becoming involved in or duplicating levels of planning and management which are more efficiently undertaken at the institutional level."
The two organisations now believe the Executive has avoided these pitfalls.
The Bill makes it clearer that the council is to be a funding not a planning body, and it will not be allowed to encroach on the responsibilities of institutions.
One of the remaining concerns is that the Bill enables the council to approve additional bodies to fund beyond the existing colleges and universities. The ASC and Universities Scotland believe this power should rest with ministers and that the council should only have an advisory role.
Controversy over section 8 of the Bill, which appears to give ministers power to introduce top-up fees, does not excite the further and higher education leaders. They feel it simply permits ministers to specify a different fixed fee for certain subjects such as medicine, and this will only be done where there is a clear case.