The overall drop was matched by a 4% decline in applicants from the United Kingdom, which Shakira Martin, president of the National Union of Students, said evidence the government "urgently needs to review the education funding system". But applications from other countries have risen by 2%.
Sarah Stevens, head of policy at the Russell Group, said it would be a concern if European Union students were being put off by the uncertainties of Brexit.
One field showing a dramatic loss of demand is nursing. However, all top three source countries showed a decrease.
The figures show a sharp decline in those applying to study nursing courses - down 19% - and a continued fall in the number of mature students, notably in England and Northern Ireland.
Dame Julia Goodfellow, president of Universities UK and vice-chancellor of the University of Kent, said there are number of issues to address.
"Some have claimed that rising fees and the lack of proper financial support for students have not deterred people from attending university", she said.
"We recognise also the concern about the total cost of going to university". Any analysis needs to cover the cost of maintenance and the interest rate on the loans, she said.
"However, the Scottish Government's recent decision to give universities the power to replicate English fee rises for students from the rest of the United Kingdom has the potential to damage our sector's positive reputation in the future".
Pam Tatlow, chief executive of MillionPlus, said the application data from Ucas was "not good news".
The EU market has been an area of consistent growth in recent years and the 5% fall in applications will create additional concerns, she said.
Overall, the number of people who applied to university courses by the June deadline was 649,700, down about 25,000 on past year, according to the admissions service.
The number of English students applying across the United Kingdom has fallen by five per cent.
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Across the United Kingdom, the numbers applying to go into higher education have fallen by 5% in England, 4% in Northern Ireland, 1% in Scotland and 5% in Wales.
There was also a marked difference across age ranges.
However, the number of applicants at the June deadline who were aged 19 or older fell 27,180 on a year ago, while in England there were 18 per cent fewer applicants aged 25 or over.
In England, the proportion of the 18-year-old population who have applied to higher education, the application rate, has increased from 37.2% in 2016 to 37.9%, the highest level recorded.
Across the United Kingdom, at ages of 19 and older there were some significant signs of falling application rates: at 19 the rate change was -5%, at 20-24 it was -7%, at 25-29 and 30-34 it was -14% and for 35 and over it was -15%. There are several possible reasons behind the drop in numbers.
There has also been a fall in the number of 18 and 19 year olds across the United Kingdom population since 2010, Goodfellow added.
It is lower-tariff universities - those admitting students with the lowest entry grades - that have been hit hardest by the downturn in applications from the United Kingdom and other parts of the EU.
University leaders said a number of factors could be fuelling the fall in applicants, including Brexit, higher fees and funding changes for trainee nurses and midwives. In 2010, universities generated just £37m from tuition fees.
He added: "How these trends translate into students at university and colleges will become clear over the next six weeks as applicants get their results and secure their places, and new applicants apply direct to Ucas' clearing process".
There are some unexplained variations in the UCAS statistics.
It is the first decline in applications since tuition fees in England were raised to £9,000 in 2012, and comes ahead of an increase in English fees to £9,250.
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