Thousands of students are being put off applying to university by the move to triple tuition fees to £9,000, an independent panel has found.
Early indications show that the fee increase, due to be introduced next month, has led to a drop in applications to English universities, experts said.
The latest evidence, published by the Independent Commission on Fees, is likely to fuel concerns about the long-term effect of the rise.
But as the report was published, the Government defended its decision to raise fees, insisting that there is still "very strong demand" for university.
The commission, which was set up in January to examine the impact of the fee hike, compared UCAS application figures in 2010, before the new regime was announced, with those of 2012, the first year that students will be directly affected.
Its first report reveals that applicant numbers to English universities are down 8.8% compared with two years ago - around 37,000 fewer students.
Among 18 and 19-year-olds, applications have fallen by around 7% over the same two-year period.
It suggests that this drop cannot be wholly explained by a reduction in the number of young people in the UK, and that the falls in England have not been replicated in other parts of the UK.
Both Scotland and Wales have seen a rise in applications (1% and 0.3% respectively) while Northern Ireland saw 0.8% fewer applicants.
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.
The report also says that separate UCAS figures suggest that among English 18-year-olds alone, changes in applications mean that around one in 20 people who would have been expected to apply to university this year did not do so - the equivalent to around 15,000 "missing" applicants.
Commission chairman Will Hutton said that although it is too early to draw firm conclusions, there is "initial evidence" that higher fees will have an impact on applicants' behaviour.
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.
"The fall in population of 18 and 19-year-olds is a significant factor in explaining some of the overall decline in applications, but this is relatively constant across the UK, and cannot account for the difference in application drop-offs between the four home countries."
The findings come just a week before A-level results are published and would-be students learn whether they have secured a university place.
Mr Hutton told BBC Radio 4's Today programme that there is a "discernible difference" across the UK.
"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."
Universities Minister David Willetts said the Government accepted that after a peak last year, applications are down, with 30.6% of people applying for degree courses compared to 31.6% in 2011.
"That is actually still the second highest rate of applications on record," he told the programme.
"We still have very strong demand for university."
Mr Willetts insisted that the new system, which sees students pay their fees once they have graduated and earning £21,000 a year, is fairer.
The commission did not find evidence of fewer applications by teenagers from poorer homes.
Mr Hutton said: "Although it is too early to draw any firm conclusions, this study provides initial evidence that increased fees have an impact on application behaviour."
He added: "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."