Comptroller and Auditor General Seamus McCarthy has said he will investigate issues raised by a whistleblower regarding an internal audit of the Central Bank.

Speaking at the Public Accounts Committee Mr McCarthy said the issues went back to matters which the Comptroller and Auditor General had raised with the Central Bank.

He said the Central Bank had decided to conduct an audit which would cover remuneration, risk management, tax and compliance.

Mr McCarthy said he had been made aware that there had been a whistleblower issue in relation to the internal audit.

The Central Bank whistleblower, who has claimed he was told to delete critical findings in an audit report about the bank, has made a protective disclosure to Sinn Féin Deputy Leader Mary Lou McDonald.

The TD raised the issue at the Public Accounts Committee and with the Comptroller and Auditor General.

Details of the former internal auditor’s claims have been seen by RTÉ News.

He alleges his contract was terminated as a result of his complaints.

However, it is understood the Central Bank argued he had come to the end of a fixed-term contract, while the former staff member maintained it was open ended arrangement.

The whistleblower claims he was told to remove his findings from a final version of an internal audit report in November 2014.

The former staff member made a protective disclosure to the then governor of the Central Bank, Patrick Honohan, under the bank’s "Speak Up" procedure, which affords protection for whistleblowers.

In a statement this evening, the Central Bank defended its internal audit mechanisms, saying it expects the highest standards of corporate governance in the firms it regulates and also applies those high standards to itself.

The Bank confirmed that a report into its compliance with the Code of Practice for the Governance of State Bodies in January had identified some deviations and some areas of control weakness which required remedial action.

These issues were reported to the Bank's Audit Committee and the majority of these remediation actions have now been completed, the statement said.

The bank added that it investigates all concerns raised by staff through its confidential disclosure policy relating to perceived wrongdoing.

It says employees are not discriminated against as a result of raising a concern.

The bank hired consultants Deloitte to examine the issues raised by the whistleblower.

Deloitte found in favour of the Central Bank’s management in December 2014.

The following month the whistleblower’s contract was terminated by the Central Bank.

The Bank told him it was a fixed-term contract and he was no longer required.

After leaving the Central Bank, the whistleblower took a case to the Workplace Relations Commission.

The draft internal audit report, written in October of 2014, criticised a lack of appropriate monitoring of arrangements for engagement of external auditors, ineffective monitoring of the banks internal auditing arrangements and lack of review of its internal audit manual.

These findings were not included in the final report, however one issue was raised in a separate memo.

The whistleblower contacted the Association of Chartered Certified Accountants, of which he was a member.

The ACCA wrote to the whistleblower and said: "At no time, even for minor matters, should matters be suppressed."

It added: "If you were asked to delete or suppress findings from the internal audit report... you should refuse to delete them and bring the matter and the request to suppress the findings to the attention of the audit committee."

In January 2015 the Central Bank completed its final Internal Audit report.

It said the Central Bank was only partially compliant with requirements. The final version retained some findings from the draft report. It said there was an absence of expertise available to the bank’s risk committee.

It also noted shortcomings regarding how the Central Bank handled its code of ethics. It said there would be steps taken to ensure absences at board subcommittees would be monitored.

The issue regarding the whistleblower’s claims is not the first time the Central Bank has been accused of suppressing findings in reports.

Frank Browne, the Central Bank’s former head of financial stability, told the banking inquiry that his warnings during the boom were "doctored" and "censored" by the bank’s management under former governor John Hurley.

Mr Browne said his claims were not made public because more weight was given to those who argued that Ireland was not facing a crisis.

Speaking on RTÉ’s Morning Ireland earlier, Ms McDonald said she had a number of concerns in relation to the information she received, which she described as being non-compliant in relation to the standards that would be expected within any state body.

"Firstly that an auditor within the Central Bank would be asked to remove or to delete findings from an audit report. That sounds alarm bells in my head,” she said.

"Secondly, on the issue of the treatment of this person of as a whistleblower. And thirdly, I would have big concerns around the lack of compliance of the Central Bank with governance standards."

When asked about the issue, Tánaiste Joan Burton said she believed the PAC was the appropriate place to take the issue.

She said she was not familiar with the details as they were still emerging.