The former chief executive of the Serious Fraud Office received £412,000 in pension and severance payments without proper authorisation, the Whitehall spending watchdog has said.
The National Audit Office ruled that the payments made to Phillippa Williamson when she took voluntary redundancy earlier this year were "irregular".
As a result, it said it was "qualifying" the SFO's annual accounts for 2011-12.
The head of the NAO, Amyas Morse, said: "By failing to seek approval from the Cabinet Office and the Treasury, the Serious Fraud Office entered into an agreement which forced it to make irregular payments.
"While positive steps have been taken by the incoming director, I have qualified the organisation's accounts."