Admissions tutors and schools claim they have been undermined and potential students misled by the head of the Universities and Colleges Admissions Service.
Ucas chief executive Tony Higgins wrote to schools saying that pupils who did not declare their AS-level results would be disadvantaged. Admissions tutors have said it is up to individual universities to decide who to admit and why.
In the letter, Mr Higgins states: "It is my personal view that those students who do not accept certification of their AS-level results and therefore do not have a qualification to enter on the application form, will be at a disadvantage.
"If pupils refuse certification then they have nothing to declare and the inference might be drawn that they have refused certification because they have done badly and that therefore they are potentially poor students."
Nigel Percival, deputy director of educational liaison at University College London, said: "We, along with most other universities, have been attempting to re-assure applicants over the issue of AS certification.
"It is an issue that has caused considerable angst in schools and colleges over the past few months. We have said that while certificated AS-grades cannot be ignored, students who are unable to provide certificated grades will not be disadvantaged.
"There are perfectly good reasons why a student may not have certificated AS grades. We have also emphasised that the relationship between AS performance and performance at final A level has yet to be established. Consequently, even when certificated AS grades are available, these should not be a key factor in determining whether or not a candidate is invited for interview or offered a place.
"It is most frustrating to have the efforts that we and other universities have made to reassure applicants, schools and colleges, undermined by Mr Higgins. I feel it was most inappropriate for him to offer this kind of ad hoc guidance at this time."
John Dunford, general secretary of the Secondary Heads Association, blamed Ucas and the universities for the confusion surrounding the status of the new qualification.
He said: "A plague on both their houses. Tony Higgins's letter will add to the confusion rather than reduce it. It is also perfectly possible for universities to encourage breadth by saying that entry grades would be three grade Bs or, if you were doing a fourth subject to AS level, two Bs and a C. I really have lost patience over this issue."
Mr Higgins's letter also irritated admissions staff and school teachers by claiming: "I believe that the new key skills qualification will become an essential criterion against which selection should be judged within the next two or three years."
Jacqueline Henshaw, head of undergraduate recruitment and admissions at the University of Manchester, said: "Predictions concerning the likely changes in admissions requirements to universities are, I believe, best based on informed intelligence from those with responsibility for determining what they are looking for in the students they admit."
* Ucas is to set up admissions systems in South Africa and the Czech Republic.