Some student loan repayments, taken from graduates' pay packets, have failed to get through to the Student Loans Company.
And interest has been added to the graduates' loan accounts, as if they have paid nothing back.
The Inland Revenue said it was urgently investigating the problem.
It came to light after a graduate contacted the Student Loans Company to find out her outstanding balance.
Computer problems
For two years she had been paying off her loan under the new system, where the money comes straight out of the pay packet.
Her pay slips showed that she had repaid £1,800 ($2,742).
But to her horror, the Student Loans Company said nothing seemed to have been repaid at all, in fact interest had been charged on the full amount of her original loan.
When she told the BBC about the fiasco, inquiries uncovered a problem with the Inland Revenue's computer systems.
Details from employers showing student loan repayments had reached the Revenue, but those details hadn't been passed on, as they should have been, to the Student Loans Company.
The Revenue said it very much apologised to any graduates affected.
And it assured them that once the problem was resolved, none of them would lose out financially.