Up to 50,000 sixth-formers will be denied places at university this autumn because of a surge in applications combined with a freeze in undergraduate places.

Vice-chancellors and the head of the admissions service warned yesterday of a looming crisis, with many popular courses already full. Nearly one in ten applicants could be left without places at a time of bleak employment prospects for school-leavers.

The number of places available through the clearing system — which gives students who missed their A-level grades another chance to apply — will be restricted severely.

University heads accused ministers of threatening them with big fines if they took on too many students while encouraging more teenagers to apply.

John Denham, the Universities Secretary, has written to vice-chancellors ordering them not to offer any extra student places. He warned that universities which did increase their student numbers could have funding clawed back. Universities fear that they will be penalised by up to £10,000 for each extra student.

Baroness Warwick of Undercliffe, the head of Universities UK, which represents vice-chancellors, has written to the Chancellor saying that without a rethink thousands of students would not get a place this year. “Many institutions will not enter clearing, and the impact on students from lower socio-economic groups will be most pronounced,” she wrote.

“The threat of fines, which may go into several millions for institutions who accidentally over-recruit, means that most institutions will aim low, possibly even under-recruiting, in order to avoid crippling financial penalties. Anthony McClaran, head of Ucas, the admissions service, told The Times: “Pressure to obtain a place in clearing will be greater than in the past. There may be less flexibility this summer and fewer places available in clearing. It’s essential that universities communicate very clearly what is and isn’t available and students are realistic in what might be available. There are not suddenly going to be places opening up in courses which are very popular.”

The plight of some students could be exacerbated by a new policy that will allow those achieving better than expected A levels to reapply to more eminent universities in August. This could offer false hope, as the best universities are likely to be full by then.

By January this year there were 464,167 applications for full-time undergraduate courses starting in September — 33,678 more than at the same time last year. More applications are expected before August.

The Government has made provision for only 10,000 more places this year, including those taken by postgraduate or part-time students and any surplus students taken last year.

Last year 132,062 prospective students were not placed in universities either because they declined their offer or missed their grades. This year the figure is set to rise to more than 180,000 as a result of the increased applications and the effective cap on undergraduate places, meaning that good students who would in other years have got places will miss out.

David Willetts, the Shadow Universities Minister, said: “It’s a cruel trick on young people, who are being encouraged to do applications when there are not enough places.”

A spokeswoman for the Department for Innovation, Universities and Skills, said university funding was at its highest ever level. But she added, “Getting a place at university is, by its nature, a competitive process and that means that there will be some people who cannot get the place they want.”

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