The Director General of the Russell Group, representing 20 leading UK universities, has said that a new study which found a 8.8% decrease in university applications is "misleading".
Wendy Piatt said that despite the drop, the application rate is still "very high".
Independent Commission for Fees chairman Will Hutton has told ITV News that a new report showing university applications down by 8.8%, is a "storm warning" that less students are "willing" to apply to university.
The Government's decision to treble university fees are "putting thousands of people off" applying to university, Shadow Universities minister Shabana Mahmood said today.
Commenting on the Independent Commission on Fees report, which found that university applications are 15,000 lower this year, Ms Mahmood said:
"The Tory-led Government’s decision to treble tuition fees at the same time as cutting funding for higher education is already putting thousands of people off university who otherwise would be eagerly preparing to start their courses".
Universities Minister David Willetts has defended the Government's decision to treble university tuition fees after independent experts said fewer younger people were applying for courses.
Speaking a week before A-level results are published, Mr Willetts said: "We do accept that after a peak last year, applications are down from 31.6% of people applying to university to 30.6%. That is actually still the second highest rate of applications on record."
Mr Willetts said the new system was still fairer and "much more like income tax", with repayment starting once students earn £21,000 a year.
The Government defended its decision to treble university tuition fees after independent experts said fewer young people were applying for courses.
An independent commission was set-up to establish whether there is any link between student numbers and tuition fees, which the Government has raised to a maximum of £9,000 a year.
Independent Commission for Fees chairman Will Hutton told BBC Radio 4's Today programme:
University fees are not going up in Scotland, Northern Ireland and Wales and the long-term trend of rising applications that we have seen in England is carrying on in Scotland, Northern Ireland and Wales. There is a discernible difference.
Nearly three-fifths of young people say the fees increase has influenced their decision about whether to apply to a university in the UK, according to a survey of around 1,000 teenagers.
The poll, published by the Independent Commission on Fees alongside its report, reveals that just under three-quarters of 15 to 17-year-olds in England say they are likely or fairly likely to apply to university.
– Liam Burns, president of the National Union of StudentsThe applications cycle for the first group of students facing a new, hideously complicated and unstable funding system, scarce opportunity and high unemployment remains incomplete.
We don't yetknow whether or where those who have applied will study.
After next week's A-level results the clearing process will commence, and we remain concerned that applicants, particularly those from certain backgrounds, may not be in a position to choose whether and where to study, based on the right course and university for them.
In England, university students are eligible to pay tuition fees to a maximum of £9,000.
Students from Scotland attending Scottish universities do not pay fees, while the Welsh Assembly has said it will pay fees above £3,465 for Welsh students attending any UK institution.
Fees for students from Northern Ireland are also capped at £3,465.
– Independent Commission on Fees chairman, Will HuttonAlthough it is too early to draw any firm conclusions, this study provides initial evidence that increased fees have an impact on application behaviour.
There is a clear drop in application numbers from English students when compared to their counterparts in Scotland, Wales and Northern Ireland.
On a positive note, we are pleased to see that at this stage there has been no relative drop-off in applicants from less advantaged neighbourhoods.
We will continue to monitor a range of indicators as the fee increases work their way through the system.
The report by the Independent Commission on Fees shows that the fall in applicant numbers in England has not been replicated in other parts of the UK.
Both Scotland and Wales have seen a rise (1% and 0.3% respectively) while Northern Ireland saw 0.8% fewer applicants.
The report concludes: "The decline in English applicants from the 2010 level was 8.8%, as compared to a nearly-constant level from the other home nations across this period. This may indicate a link between the level of tuition fees and the numbers of applicants.