Staff costs at the regulator were £15.4m higher than budgeted for following its decision to make a one-off contribution of £22m to reduce its defined benefit pension scheme deficit.
The figures are revealed in the final annual report of the FSA, which was replaced by the Financial Conduct Authority (FCA) on 1 April.
During the year to 31 March 2013 the FSA strengthened senior staff levels with the recruitment of five new directors and 30 new heads of department to drive the new organisational structures follwoing the transition to the FCA.
"Having hired talented staff, the FSA continued to develop them through training and competency programmes and to see levels of employee engagement in line with high performing companies," the regulator said.
The regulator said staff costs were partially offset by a £6.6m under spend, driven mainly by "longer recruitment glide paths" compared to the Financial Services Authority's (FSA) budget assumptions, together with underspends on travel and recruitment.
Net ongoing regulatory activity expenditure for the year to 31 March 2013 was £528.2m, resulting in an £8.2m surplus against the £536.4m budget.
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