Four out of five universities believe top-up fees will harm the recruitment of new teachers, a TES survey reveals.
Leaders of education departments at 43 universities said the fees, to be introduced in September 2006, would hit shortage subjects hardest and push more students into on-the-job training.
Universities say numbers on employment-based courses are limited and account for just 20 per cent of teachers entering the profession, and inspectors say the quality of teaching is not as high.
Most universities said they had no option but to phase in higher fees because of continued underfunding of teacher training.
The TES poll shows that 60 per cent of universities will introduce the full pound;3,000 top-up fee for students taking the Postgraduate Certificate in Education, the most common route into teaching.
At present, PGCE students each get around pound;1,200 to cover fees. The Government has said this cash help will continue. But earlier this year Kim Howells, higher education minister, refused to rule out the possibility of students paying up to pound;1,800 themselves.
James Rogers, executive director of the Universities Council for the Education of Teachers, said: "If you ask graduates for more money on the top of debts already built up, it is going to put some of them off. The only way for the Government to lessen the impact is to put more money per head into teacher training."
The TES surveyed the English and Welsh members of UCET in February and March to gauge the impact of top-up fees. All but one of the 43 universities that responded said they did not receive enough money to cover the costs of teacher training.
The survey follows a study for the Department for Education and Skills last year that revealed courses were underfunded by an average of 20 per cent, often leaving finance departments to make up shortfalls. One university head of education told The TES: "We make extensive use of part-time staff simply to make ends meet."
A quarter of universities (28 per cent) said they had yet to make a decision on fees, in contrast to the 66 per cent that were going ahead.
Most of the rest said they would levy fees of pound;2,200 - pound;2,700.
Eighty per cent said that if students were left to pay the fees, fewer would apply, ultimately spreading teacher shortages across the sector.
Recruitment analysts warn that shortages are on the horizon as increasing numbers of teachers retire.
Some universities believe that fees will lead to more demand for on-the-job training such as School Centred Initial Teacher Training (Scitt) courses and the graduate teacher programme (GTP), although numbers on such courses are limited and account for just one-fifth of all newcomers to the profession.
The Office for Standards in Education rates the majority of university-based training highly, but feedback for employment-based training is more varied.
John Parnell, director of postgraduate training at Cardiff university's school of social sciences, said: "Expect a decline in the number, and more importantly, the teaching potential and standard of future entrants."
Viv Griffiths, director of initial teacher training at Sussex university, said: "We are concerned about the potential impact on our applications to PGCE courses. Our guess is that more people will try to apply to employment-based routes." The University of St Mark and St John, Plymouth, plans to charge a pound;2,700 top-up fee for all students, but will offer a free wireless laptop as a perk.
Jeff Battersby, dean of education, said fees would hit secondary subjects hardest. He added: "It might also adversely affect the likely recruitment of those from disadvantaged backgrounds."
Alan Smithers, professor of education at Buckingham university, defended school-based training: "If you look at the Ofsted ratings of university and school-based courses, there was a big difference at first but the quality of the school-based training has risen year on year."
The Teacher Training Agency, which attracted record numbers of graduates into the profession last year, is reviewing course funding and the possibility of increasing financial incentives for new teachers. It expects to prepare a report for Ruth Kelly, the Education Secretary, in coming weeks.
Ralph Tabberer, TTA chief executive, said: "There is some uncertainty about postgraduate variable fees but we have time to look at a range of options and to make sure we get it right.
"Teacher training has been turned round in terms of quality and performance over the past five years and we do not intend to let go of those achievements."