There is growing speculation that Scotland's new first minister, Jack McConnell, will bring together tertiary and school education under a single ministerial portfolio.
The current education portfolio covers schools, Europe and external affairs. Further and higher education are in the enterprise and lifelong learning portfolio.
A spokesperson for Universities Scotland said: "The Scottish Executive has put the commercialisation of university research at the heart of its economic-development policy and we see the continuing link between enterprise and lifelong learning as very valuable."
The Association of University Teachers Scotland said universities and further education had more in common with the business sector and were quite distinct from the schools sector.
Alex Neil, convenor of the parliament's enterprise and lifelong learning committee, said the present arrangement was better because it brought together all post-school education and training and built up the relationship between industry and academia.
Mr Neil said there was an agreement that the cross-party committee would complete its inquiry into lifelong learning.