The Government was warned a year ago that changes to student numbers would create problems in admissions, it was reported today.
Ucas, the organisation which manages applications to higher education courses, sounded the alert over the AAB system, according to documents obtained under the Freedom of Information Act by Times Higher Education.
Concern has been mounting over a shortfall in the number of undergraduates entering higher education this year.
Last Friday Ucas published figures showing a 14% fall in the number of UK and European Union students taking up places in institutions in England for 2012-13 entry compared with the same point last year.
It is reported that the loss of income from these students could cost the sector about £1.3 billion over three years.
The data also showed that 79,200 students achieved AAB grades or higher in A-level and equivalent qualifications; the predicted total was 85,000.
That leaves several of the most selective universities facing significant student shortfalls under the AAB system, introduced by the Government in the hope of allowing such institutions to expand.
Under higher education reforms, universities are allowed to recruit as many students scoring AAB or equivalent as they want.
From next year, this will apply to students achieving an A and two Bs at A-level or equivalent.
Times Higher Education reported that Ucas, responding to the Government consultation on last year's higher education White Paper, which included the AAB system, said: "Uncertainty resulting from these proposals and the timetable for making decisions on numbers of places will make it more difficult for some institutions to manage their undergraduate student numbers effectively."
It added: "The timetable for introducing the student number control arrangements for year of entry 2012 could pose challenges for learners, institutions and Ucas."
The problem of falling student numbers is thought to have been fuelled by fewer students than expected achieving top grades, and also by rising tuition fees, which triple this year to a maximum of £9,000. Another factor is thought to be that a high number of students have deferred entry until next year, while a low number did so last year.