A Central Bank whistleblower is claiming he was told to remove critical findings from an internal audit report about the bank.

The former employee, who alleges his contract with the bank was terminated after he complained, has made a protective disclosure to Sinn Féin deputy leader Mary Lou McDonald.

Ms McDonald has submitted details of the case and the report, written in October of 2014, to the Comptroller and Auditor General and plans to raise the matter at the Public Accounts Committee.

She said she was “very concerned” that a high-ranking auditor within the Central Bank would be asked to remove or delete findings from a report.

Speaking on RTÉ's Morning Ireland programme, Ms McDonald said the report reflected the bank's "partial or non-compliance" with the code of governance set out for State bodies.

She said the original report found the bank was partially compliant on the issue of staff pay.

The Central Bank has been in the spotlight over the payment of retention bonuses to some staff, which unions claim may have breached financial emergency legislation on public-sector pay.

The Central Bank hired consultants Deloitte to examine the issues raised by the individual. Deloitte later found in favour of the Central Bank’s management.

In a statement, the Central Bank said it was not in a position to comment on issue as it is currently before the Workplace Relations Commission.

“However, the Central Bank can confirm that issues raised about Internal Audit (IA) in the Bank were thoroughly investigated last year following challenges raised by a team member,” a spokeswoman said.

“ Because the matter related to the IA function, the Central Bank appointed an independent external party to fully investigate. The independent external party did not uphold the complaints,” she added.

“ The Central Bank has a confidential disclosures (‘whistleblowing’) policy in place, and places great importance of staff ‘speaking up’ when appropriate. The Central Bank is satisfied that its actions in relation to this issue have been appropriate,” she said.

The employee is understood to have detailed his concerns to the then governor of the Central Bank, Patrick Honohan, through an internal mechanism for whistleblowers.

However, Ms McDonald said she had concerns about whether the individual was treated correctly as a whistleblower.