They are also warning that universities and colleges which depend heavily on BEd students - usually the former polytechnics - could find it increasingly difficult to attract students.
John Howson, a consultant to the Teacher Training Agency, said "You could have a situation where student teachers are sitting side-by-side, with one having to pay tuition fees and the other exempted. Students will think twice about going down the BEd route."
At Plymouth University, which has 800 students on BEd courses, Professor Michael Newby said: "There is potentially a huge threat to the four-year BEd, as potential teachers realise they will save Pounds 1,000 by opting for a three-year degree and a one-year postgraduate course.
"Also, students on a three-year subject degree are more likely to lose their commitment to teaching during the course than those on the BEd, who are plunged into teaching straight away."
He said that the BEd was particularly popular with mature female students, people who are sure that they want to teach.
"We could lose these people. The Government is being too complacent about primary recruitment. We will have to wait until next September to find out how severe the problem is," he said.
Ian Kane, chair of the Universities Council for the Education of Teachers, said: "It seems very short-sighted of the Government not to give the fourth-year exemption to BEd students. Apart from exacerbating recruitment problems it could lead institutions to shorten the courses - this could lead to a dilution of standards."
John Howson said: "My guess is that in the next couple of weeks we are going to see a number of subjects where recruitment is even worse than last year, which will make the situation the worst it has been for five years."
But he dismissed recent suggestions that the training agency's "nobody forgets a good teacher" recruitment drive launched in October was not working and that it should have stated that tuition fees were to be waived. "The campaign was planned long before the fees situation became clear. It is the Department for Education and Employment, not the TTA, which has the responsibility for making the fees position clear."
A spokesman for the TTA said that enquiries from prospective teachers had doubled since the start of the campaign. "We are getting about 400 people a week filling inquiry cards at cinemas."
At her annual lecture on Wednesday, Anthea Millett, the TTA's chief executive, warned teacher-training institutions not to cultivate a "bums on seats mentality" and recruit substandard students to make up numbers.
"To them I say, lead yourselves not into temptation. Teaching is a demanding and highly-skilled profession and only good quality candidates need apply. "