Core subjects that have traditionally underpinned British universities are under threat as students choose easier options.
The new top-up fees are likely to escalate the closure of small Physics, Chemistry and Modern Language departments, warn vice-chancellors.
Only 2,905 students started Physics degrees last autumn and 3,042 enrolled for Chemistry out of a total 374,307 beginning undergraduate courses.
Media Studies, the biggest growth area this year with a rise of 15 per cent, Journalism and Publicity have overtaken the pure sciences. The latest figures from the Universities and Colleges Admission Service (UCAS) show Sports Science enrolled more students than Physics and Chemistry together.
Over the past decade, 20 out of 70 university Physics departments have closed and at least five more are under threat because of low recruitment and the Government's funding mechanism which encourages universities to concentrate on their largest and most successful departments.
The Institute of Physics warns that large swaths of the country are becoming "deserts" because of the closure of smaller departments, which makes studying the subject impossible for those who want to attend universities near home.
"It is a very serious situation because there are large areas of the country where there is no higher education in physics," says Sir John Enderby, vice-president of the Royal Society and the institute's president-elect.
"Not only is there less choice for students but parts of the country are without the expertise provided by Physicists."
Many smaller departments have been responsible for important scientific breakthroughs, he says, such as Hull's Chemistry department which pioneered work with liquid crystals and the Biologists at the University of Leicester which helped to develop DNA fingerprinting.