Almost four out of 10 courses in a group of universities are unlikely to accept students with the new Diploma, a survey of admissions officers says.
University applicants will have to decide about Diplomas or A-levels
The Diploma is being promoted by the government as an alternative to the traditional A-level.
But this survey of leading research universities says that 38% of admissions tutors are "unlikely" or "very unlikely" to accept Diplomas.
Just under half (48%) said they were "very likely" to accept them.
The first Diplomas are to be introduced this autumn - and the reaction of universities has been seen as important for their future credibility.
This survey, carried out by the 1994 Group of major research universities, gives a mixed message - saying that universities want the qualification to succeed, but warning that at present there remains considerable uncertainty about its value.
Asked about the "likelihood of accepting applicants from Diplomas to undergraduate courses", 48% of admissions tutors said "very likely", 5% "likely", 9% "possible", 2% "not likely" and 36% "very unlikely".
There are quotes from university departments about their misgivings.
"No currently-proposed Diploma has the right focus," said a maths tutor.
"At present, I would prioritise students with traditional A-level qualifications," said an education tutor.
Other comments include: "I would be unhappy to admit students just on the strength of their Diploma" and "Students interested in studying law are more likely to do A-levels."
The report also concludes that the IT Diploma "is not an adequate preparation for degree study in computer science".
This might seem like bad news for the Diploma, but the chair of the 1994 Group, Steve Smith, vice-chancellor of Exeter University, says it is more a case of universities saying "wait and see" rather than an outright rejection.
"We want to make the Diplomas work," says Professor Smith. "So we want the government to engage more closely with universities to make sure that the Diplomas can have equal esteem."
And Professor Smith says the reforms have the potential to "become a radical alternative to the existing curriculum".
This group of universities, representing the mainstream of traditional research universities such as Durham, St Andrews, Exeter, Warwick and Goldsmiths, will be a key test for the new Diplomas.
They currently admit the type of A-level students who will soon be offered Diplomas as an alternative. If these students are worried that universities are not going to value the new qualifications, it will be difficult to persuade them to change from the "gold standard" of the A-level.
And if university applicants reject Diploma courses there could be a two-tier system, in which Diplomas are seen as a vocational option, less prestigious than an academic A-level.
This will also put pressure on behind-the-scenes discussions about the relationship between the content of A-levels and Diplomas.
There have been concerns from schools about the impracticality of offering both types of course, particularly in humanities subjects - with the suggestion that the content of A-levels could become part of the Diploma.
In response to the 1994 Group report a spokesman for the Schools Department said: "Universities play a central role in the development of the new Diplomas and a number of leading universities have already signalled their support."
The Conservative universities spokesman, David Willetts, said the government should heed the warning about the value of Diplomas.
"The real value does not come from ministerial edicts but from genuine educational rigour. So universities are right to be cautious about the government's latest initiative."