The Student Loans Company is having to reimburse an increasing amount of money to graduates who have been overcharged on their loan, a BBC investigation has revealed.

The company has refunded more than £107m over the last 13 years. The average repayment to graduates who were overcharged in the year 2009/10 was £557, with one graduate receiving £96,000.

In the tax year ending April 2010, the amount of money paid back increased by 15% on the previous year, from £19m to £22m. The problem affected 40,050 graduates, compared with 36,617 the year before.

Loan repayments are made through the tax system. However, the Student Loans Company only receives information about how much an individual has repaid when employers submit annual tax returns at the end of the year. This means that graduates who pay off their loan during the tax year end up being overcharged.

Speaking to BBC Radio 4, 26 year old graduate Nicholas Lativy said: “"The amount that has been overpaid demonstrates that the system is broken.” He went on to say that in order to reclaim his money he had to make numerous phone calls and fax a number of documents.

Additionally, the number of complaints made to the company doubled in 2010/11 from those made in the previous year.

The Student Loans Company was keen to emphasise that all money was repaid with interest and that changes in the system introduced in 2009 allow graduates approaching the end of their loan repayments to switch to direct debit. This pre-emptive action gives graduates more control over their repayments, but is yet to cause a decrease in either the amount of money, or number of people overpaying. Currently, of the 106,000 students who have been offered the direct debit scheme, only 32,000 are using it.

"They shouldn't design a system in such a way that you have to be extremely attentive," Mr Lativy said on the programme.

It is likely that the trend of increasing disparities between the amount graduates should be paying and are paying will only get worse when university fees triple next year to £9000.