Fingerprinting of overseas students will begin this month - and university chiefs are warning that it needs to be a simple and efficient process.
Under tougher immigration rules designed to tackle bogus colleges, overseas students coming to the UK will need biometric identity cards.
The first students having to give fingerprints will be those applying for visa extensions from 25 November.
The government says overseas students pay tuition fees worth £2.5bn per year.
The Home Office's tightening of border controls, set out earlier this year, will include the requirement that "we check and record the fingerprints of any applicants applying for a student visa".
"All students allowed to come here will need to obtain a biometric identity card, so we know exactly who they are and what they are entitled to do."
Overseas students - classified as those from outside the European Union - have become an important source of income for universities, particularly as they pay higher fees than UK students.
The university watchdog, the Quality Assurance Agency, said earlier this year that some universities were now financially dependent on overseas students.
So there will be concerns that the introduction of tighter immigration controls, including compulsory fingerprinting, might deter potential applicants.
The higher education representative body, Universities UK, has warned that there are only six centres around the UK where biometric information can be collected - which will mean long journeys for some students.
There are also concerns about queuing times - and an absence of any way of booking an appointment.
"Despite repeated requests for information on whether there will be a booking process we have not so far received this information," said Universities UK chief executive Diana Warwick.
The changing rules for overseas students are part of a "clamp down on bogus students", announced by the Home Office, which will see colleges having to hold a licence from the UK Border Agency.
There have been widespread concerns that bogus colleges have been providing a means of falsely entering the country - allowing people to claim student visas without really studying for any qualifications.
Almost 300 bogus colleges have been uncovered in the past three years.
The Home Office expects 50,000 to 60,000 students to be affected in the first phase between now and March.
Last year, there were 313,000 applications for student visas - of which 217,000 were issued. Existing students won't be affected unless they want to extend their visa.
From next March, overseas students will need to be sponsored by a college or university holding a licence from the UK Border Agency.
From next autumn, there will be a further tightening of the rules, in which universities and colleges will use a "sponsor management system" to inform the UK Border Agency if students are failing to attend courses.
"This new route for students will ensure we know exactly who is coming here to study and stamp out bogus colleges which facilitate the lawbreakers," says Border and Immigration Minister Phil Woolas.
But he also notes that "international students contribute £2.5bn to the UK economy in tuition fees alone" - and the Home Office notes another estimate that overseas students are worth £8.5bn to the wider economy.
Baroness Warwick says that universities recognise that students cannot be exempt from immigration policy.
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