For the period ended 31 March the Financial Conduct Authority confirmed that refunded fees came to £19.5m, which was 83% higher year-on-year.
In its annual report, the FCA said the main reason for the under-spend was mainly due to the FCA not being at full headcount.
A spokeswoman for the FCA said one of the considerations taken into account when calculating the fees is its staff costs. But in 2013/2014 its head count was less than expected which resulted in a higher refund.
The regulator generated £11.3m of revenue by charging firms for interim permission applications for consumer credit, whereas no such activity was carried out the year before.
But overall the FCA made a loss of £29.3m for 2014/2013 which it said was due to deficit after tax of £2.9m and a loss of £26.4m related to its defined benefit pension scheme which was retained from its predecessor the FSA.
