At least six universities are planning to defy government guidelines and levy the extra "administration charges" to cover the cost of running the fees scheme.
Undergraduates will have to pay up to pounds 1,000 a year towards the cost of their education for the first time from October.
Most universities are allowing students to pay the fee in two, three or more instalments. But it emerged yesterday that six institutions - Stirling, Liverpool, Aston in Birmingham, Kent, Manchester and Glasgow - are planning to charge for the privilege.
The National Union of Students attacked the plans, saying they would hit the poorest students. The union appealed to all universities to allow students to pay the fees by instalments.
NUS president Andrew Parkes said: "We are recommending that all fees should be payable by a minimum of three instalments and there should be no administration fee. Institutions should also publish very clear regulations governing the collection of fees."
A spokesman for the Department for Education and Employment said administration fees were "strongly discouraged", arguing that central government grants to universities should cover the pounds 8m estimated cost of administering the scheme.
DFEE guidance sent out to universities last month made it clear that the department "does not see a case for institutions charging administration fees to students who pay by instalments". The Teaching and Higher Education Act, which introduced the fees, effectively bans universities from making "top-up" tuition charges, but leaves institutions to decide how and when to charge the fees, and what sanctions to impose on those who fail to pay up. A DFEE spokesman said: "We strongly discourage institutions from charging administration fees. Grants that universities receive include an amount to compensate for payment by instalments. There should be no need for any extra fee."
But Stirling University finance director John Gordon said the university had been forced to take on two more staff to administer the collection of fees. "It is nonsense for the Government to say that its grants to universities cover these costs," he said.
Universities making no charge include Newcastle, Leeds, Leicester and the London School of Economics. Kevin Gleeson, fees manager at Leeds University, said the university had budgeted pounds 250,000 to set up its collection office, but insisted there would be no charge for paying the fees in instalments.
He said: "We have decided to be fairly easygoing to students in the first year."
A spokesman for the Committee of Vice-Chancellors and Principals, which represents universities, said: "Universities are offering a number of ways of paying tuition fees. Some are offering discounts for early full payment, others are charging students for paying by instalments.
"The additional burden of collecting money by instalments may cost more than the Government allowance of five per cent."
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