The head of the HSE says the body may need to make a 'technical financial adjustment' for 2021.
However Paul Reid denies there is a 'black hole' in the executive's finances.
It follows a leaked recorded meeting between the Department of Health and the HSE, which raised concerns about 'fake targets' and 'serious financial governance issues'.
The Business Post says it obtained a recording of an internal Department of Health meeting where officials expressed concerns over "chasing fake targets", the wider recruitment crisis in the HSE, "sloppiness" around financial reporting and "hundreds of millions" of adjustments for "fundamental errors" in past accounts.
Mr Reid told Newstalk Breakfast the comments are "factually incorrect".
"My general reaction is it certainly doesn't reflect the very good collaboration that goes on between ourselves in the HSE and the Department of Health at all levels.
"Specifically related to the comments: they are disappointing, but they are actually factually incorrect."
On the finance issue, he says any adjustment would be less than €100m.
"There will be no adjustment of hundreds of millions planned in our accounts for last year.
"It's never been indicated, there is no black hole.
"The reality of what is happening is there's a process initiated by ourselves... around looking at the subset of our accruals and our provisions at the end of 2020, and what was the cash management that we carried forward into 2021.
"In essence when we deep dive into some of that, it would indicate we may possibly need - and this hasn't been confirmed yet - to make a technical financial adjustment for 2021.
"It won't be in hundreds of millions - if we do need to do it, it'll be less than €100m.
"And an important point to say: it's not an increase in expenditure, it'll actually reduce reported expenditure.
"And it is a process we would work through with then C&AG, it is a process we would work through with our boards, it is a process we would work through with our audit and risk committee".
Taking the recruitment issue and claim of fake targets, he says the HSE will strive for 10,000.
"The reality of recruitment in the HSE, in the past two years - from 2020 to 2022 - we've recruited 12,500 people".
He says when contact tracing workers are included, this number increases to around 24,000 over the last two years.
"So when we looked forward into the recruitment projections for 2022, a funding stream is there for 10,000 - which we would hugely welcome.
"What we did reflect back to the department is the reality of the recruitment market at the minute - and particularly in the health sector - it's a global demand for health professionals".
He adds that while market projections suggest recruitment of "about 5,500", "we would strive to achieve the 10,000 and that's what we're striving to do".