Writing in the journal Scottish Affairs, Professor Gallacher says the failure to plan links between Scotland's parallel systems is limiting opportunities available to students, and "prevents our HE system making its full and most effective contribution to Scottish society.
"There is now a pressing need to address these issues, and take steps which will ensure a more effective integration of these systems, whilst recognising their distinctive traditions and contributions."
Iain Gray, Lifelong Learning Minister, has already thrown his weight behind the "two-plus-two" approach. This would allow higher national certificate students to be accepted into university second years and higher national degree students to move straight into the third year of a course.
HN qualifications are taken by a quarter of all HE students, but links with degree courses are embryonic. The newer universities, such as Glasgow Caledonian, Napier and Paisley, tend to collaborate more closely with FE colleges than the ancient universities.
Most links involve "articulation" arrangements between individual universities and groups of colleges; the universities simply agree to give priority in admissions interviews.
This is far from the "advanced standing" Mr Gray envisages, which would guarantee entry to the second and third years of equivalent degree courses.
Professor Gallacher argues that curricular and cultural issues hinder the smooth progress from HN programmes to degrees. Some university admissions tutors complain that students lack the underpinning knowledge required for courses, while colleges say there is too much emphasis on knowledge and not enough on capacity to learn.
He also says that problems arise because students are not prepared for university life, particularly the larger institutions and classes they encounter, but also different methods of assessment and teaching. One study found that as many as two-thirds of students moving from college to university ran into one or more of these difficulties.
This led some HE staff to the conclusion that the students were not cut out for degree work, which confirmed scepticism about the value of entering agreements with colleges on advanced standing.
The difficulties are compounded by funding differences, Professor Gallacher says. Full-time courses in universities attract pound;3,900 per student, compared with pound;2,900 in colleges, according to Scottish Executive figures last year. Colleges argue that this makes it difficult to offer the same quality of experience.
Professor Gallacher says it is imperative these underlying issues are tackled if the Scottish Credit and Qualifications Framework, which is intended to ease transfer and progression, is to stand any chance of success. The framework is a major plank in the final recommendations likely to emerge from the report of Holyrood's lifelong learning inquiry next month.