The Wales Audit Office (WAO) says claims it has deliberately over-billed public sector bodies or taken money for work not carried out are "wide of the mark."
Responding to a newspaper report, it said there was often variation between planned work and what was actually delivered in any year.
It said the claims would hit the morale of its "hard working staff."
The results of a review into the WAO go to the Welsh Assembly next month.
The WAO ensures billions of public money in Wales is spent correctly.
The Western Mail has claimed public sector bodies in Wales have been charged millions of pounds for work that was not carried out.
But the WAO said with around 1,000 audits carried out each year there was often changes to planned work and what actually happens in any specific financial year.
It said changes were often at the request of individual public bodies with work amended during the year or transferred from one year to another with appropriate accounting adjustments.
"The suggestion that the Wales Audit Office has deliberately over billed in this way or retained money for work not carried out is wide of the mark," it said in a statement.
The results of the National Audit Office investigation will be presented to the assembly's Public Accounts Committee on 9 December.
It was requested by the new auditor general for Wales Huw Vaughan Thomas.
He succeeded Jeremy Coleman who resigned in February after he was arrested for having indecent images of children. He has subsequently admitted 14 charges.
The WAO said following discussions with union representatives Mr Vaughan Thomas also encouraged all staff to approach the investigative team in confidence, if they had concerns relating to the accounts.
"It is extremely disappointing and somewhat troubling that members of staff have chosen to go directly to the press in an anonymous fashion rather than share any information for thorough investigation," it said.
Mr Vaughan Thomas said he was concerned the allegation would "impact . . . on the morale of our hard working staff."
He added: "Whatever some individuals may think, the people of Wales can, I believe, share my confidence in the quality of the work, dedication and integrity of the staff of the Wales Audit Office."