The number of full-time students enrolling at English universities fell by 2 per cent in the year that top-up fees were introduced.
Statistics from the Higher Education Statistics Agency show that 502,190 first-year students started university in England in 2005-06, but the figure dropped to 492,865 in 2006-07.
In the same period, enrolments at Scottish and Welsh institutions - where there are no top-up fees - increased by 3 per cent and 4 per cent respectively.
In Northern Ireland, where students pay top-up fees, the drop was 9 per cent.
Bill Rammell, Minister for Higher Education, said this was only a "small anticipated decrease", adding the trend was "strongly reversed" with the number of acceptances for 2007-08 recorded since.
"The Government is committed to unlocking the talents and potential of all our young people, ensuring that a university education is an option for everyone," he said.
He added that a 10 per cent increase in entrants from non-European Union countries showed the UK remained an extremely popular destination for international students. He also welcomed the increase in foundation degree awards to students at higher education institutions, up 25 per cent between 2005-06 and 2006-07 to 11,635.
"Foundation degrees are a core part of our strategy for growth in higher education and represent the sort of employer engagement we want to encourage more widely. We are well placed to see further increases to meet our aspiration of 100,000 students enrolled on foundation degree courses by 2010," Mr Rammell said.
The University and College Union, which is opposed to fees, said the figures proved that poorer students were put off by top-ups.
Sally Hunt, general secretary of the UCU, said: "Anyone who really believes that charging more for degrees is the way to encourage students to apply to university is living in a dream world."