While they believe a merged council will help improve links between further and higher education, they have "serious concerns" about the draft Bill.
"The main message we want to convey here is that we have a shared view that parts of the draft bill are misconceived because they increase the role of the funding body at the expense of those of governing bodies," the joint submission states.
They warn ministers that the new council must be "lean and efficient", smaller than the two existing bodies, that it must not become involved in planning or micro-managing further and higher education, and that there must be no political interference in matters that are the responsibility of governing bodies.
The chief concern of the universities is the creation of Steps, (Specified Tertiary Education Providers), which is a status that all colleges and universities must achieve to be eligible for public funding - and which may be open to private providers as well.
This potential for competition has already sparked fears and there are also concerns that the four categories in the Steps framework could re-create a binary line between Scotland's ancient and modern universities.
Tom Kelly, chief executive of the Association of Scottish Colleges, said:
"If we get this right, it is a chance for us to make lifelong learning more of a reality where it matters most - in the colleges and universities and for the learners that they serve. A small, smart and strategic funding body as we have outlined will deliver greater benefit to learners, employers and Scotland as a whole."
Bill Steveley, convener of Universities Scotland, said the fact that this is the first joint policy statement from the two sectors "is a clear message that there are real and justifiable concerns with these proposals as they stand".
Lewis Macdonald, Deputy Lifelong Learning Minister, has already promised to reconsider areas of concern before the proposals reach the legislative stage.