The number of students going to university has fallen since variable fees were introduced, statistics show.
The figure dropped back to 40% of the 17-30 age group in 2006/07 from a high of 42% the previous year.
The Department of Innovation (Dius), Universities and Skills says it views this is a temporary setback.
Lecturers say the figures should serve as a warning to the government on the effects of fees on students.
The figures, released by Dius, relate to the Higher Education Participation Rate (Heipr) for first time students who came from homes in England and went to universities in the UK between 1999/2000 up to 2006/07.
They also cover English-based students who went to English, Welsh and Scottish further education colleges.
The figures have fluctuated marginally from 39% in 1999/00 to 40% in 2000/01 and the following year, rising to 41% in 2002/03, then falling back to 40% in the following two years.
"The drop in students in 2006/2007 from the previous year must serve as a warning to the government as it prepares next year's review into the impact of top-up fees"
A high of 42% was reached in 2005/06 before falling back to 40%, according to provisional figures for 2006/07.
Annual tuition fees - which used to be a flat rate of £1,175 - have, since September 2006, been varied from nothing up to a maximum of £3,000 a year, index linked.
Higher education minister Bill Rammell said acceptances and applications to higher education in England were at an all time high.
He said: "We have known for a long time that applications fell in 2006/07 which coincided with the introduction of variable fees - this has led to the reduction in the Heipr.
"But acceptances have recovered strongly with 17,730 more students accepted in 2007, taking the total from 289,229 in 2006 to 306,959.
"The figures for applications for 2008/09 are also up over 7% on this time last year – that is at least 20,700 more applications.
"A year from now we expect the counterbalancing rises of 2007/8 to increase the Heipr.
"These figures clearly show that variable tuition fees are not deterring people from applying to HE, as the doom-mongers predicted."
Alarm bells
The University and College Union (UCU) said the government was in no position to slap itself on the back.
UCU general secretary Sally Hunt said: "The self-congratulatory remarks of Bill Rammell about applications and acceptances since 2006/07 are ill-judged, given these latest participation figures.
"The drop in students in 2006/2007 from the previous year must serve as a warning to the government as it prepares next year's review into the impact of top-up fees."
Universities UK, which represents the interests of higher education establishments, is not too concerned about the figures.
A spokesman said: "These figures relate to 2006/07, the first year of the new fees regime in England.
"There was a small downturn in applications, perhaps unsurprising given that a new system was being introduced.
"But as the latest UCAS figures show, applications to universities in England for 2008 are at an all time high.
"This also follows a record number of students accepted onto courses for 2007/08 entry."
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