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University applications for 2012 are running at 9% below last year's level, says the Ucas admissions service.
When overseas applications are taken out, the figures show a 12% drop in applications from UK students.
These are the first official application figures for students who will be paying higher tuition fees.
Universities UK cautioned that with months before the final application deadline such preliminary figures remain "unreliable indicators".
The final deadline for most courses is January - but Oxford and Cambridge and medical school applications have now closed and these showed a 0.8% fall.
Impact of fees
The Ucas figures show applications to UK universities up to 19 October - and they will be scrutinised to find an early indication of the impact of raising fees to up to £9,000 per year for many English students.
But this early evidence shows a mixed picture.
The headline figure of a 9% decline also includes an increase in overseas applications - and the drop for UK students is 12%, higher than some surveys had anticipated.
But within the UK, the drops in England and Scotland are both 12%, even though Scottish students will not have to pay tuition fees.
The figures show that about 7,000 fewer students have applied at this point compared with last year - with the biggest declines among mature and female applicants.
Applications from people over the age of 25 have fallen by more than a fifth, the Ucas figures show. Among those in their forties, the drop is 28%.
Les Ebdon, chair of the Million+ group of new universities, warned of the importance of mature students not being put off university.
"Studying for the degree people need to get the job they want in the future will be particularly important for those seeking to re-enter the labour market after losing their jobs," said Professor Ebdon.
"It's too early to read into these figures at the very start of the applications process," said Nicola Dandridge, chief executive of Universities UK.
But the leader of the UCU lecturers' union, Sally Hunt, linked the fall with the sharp increase in fees.
"The government's fees policy has been a disaster from the start and it is clearly having a serious impact on the choices young people make," she said.
Universities minister David Willetts said an information campaign for schools and colleges about the student finance system would be extended.
"It is important that no one is put off applying to university because they do not have information about how the new student finance system works," he said.
Toni Pearce, vice-president of the National Union of Students, said: "The indication is that the confusion caused by the government's botched reforms is causing young people to at the very least hesitate before applying to university."
Ahead of these preliminary Ucas figures, a survey commissioned by BBC Inside Out suggested that higher fees will put off 10% of potential students in England.
The survey of 1,009 A-Level students found most would probably still go to university despite higher fees.
But about half said they would consider selecting a university closer to home to cut living costs, or one abroad with cheaper fees.