But a statement from Dr Cooper's office said all whistleblower disclosures were treated with respect and the auditor-general would not be resigning. Documents show Dr Cooper's office decided not to proceed with the public interest disclosure investigation into allegations the whistleblower made about the decision making process to enlarge the Cotter Dam. Correspondence shows the lack of communication with the whistleblower about the closure of the investigation breached the audit office's own public interest disclosure procedures.

While documents from the audit office say the investigation was closed, the whistleblower himself was this year given conflicting reports about whether the public interest disclosure process was still open or closed. Varying accounts were given to him by the ACT Ombudsman's Office and the audit office.

This happened despite strict PID procedures requiring whistleblowers to be informed about investigations into issues they have raised every three months and informed of any grounds as to why an investigation has been stopped.

It appears as though the audit office decided to cover some of the issues raised by the whistleblower in a separate performance audit relating to the Cotter Dam.

The documents show this did not go into all the whistleblower's concerns, particularly about the processes leading up to the decision to enlarge the Cotter Dam, and that the whistleblower did not know the PID process had been closed in favour of looking into the issues in a performance audit.

Professionals Australia ACT director David Smith said whistleblowers who came forward in the public interest "deserve much better than this".

Professionals Australia has already said Dr Cooper should not have signed off on last month's audit into the expanding of the dam due to a conflict of interest.

In 2007 Dr Cooper chaired a taskforce recommending the dam be enlarged but the audit office denied there was a conflict of interest.

"For the auditor-general to be also involved in the investigation of a public interest disclosure into similar matters, including the apparent shutting down of that process, without disclosing or acting on their clear conflict of interest is outrageous," Mr Smith said regarding the whistleblower documents.

"We have lost confidence in the auditor-general and believe the only appropriate course of action for the auditor-general is to resign."

A statement from the audit office said "no one has been or is being shut down and the auditor-general is not resigning".

"The confidentiality required in the management of disclosures means that the auditor-general is unable to respond publicly to allegations about the management of specific disclosures," the statement said.

"The Public Interest Disclosure Act 2012 prohibits information obtained under the act from being used or divulged.

"All [disclosures] are treated with respect.

"Not all disclosures are able to be substantiated and therefore a discloser's desired outcome may not be realised."

The statement said the ACT Ombudsman did one investigation relating to the management of a public interest disclosure managed by the ACT Audit Office.

"The ACT Ombudsman advised that 'no further investigation of this case is warranted'," the audit office said.

"The Independent Competition and Regulatory Commission's consideration of the Enlarged Cotter Dam [Enlarged Cotter Dam Water Security Project – June 2010] combined with the audit office's audit [Bulk Water Alliance – June 2015] means that costs have been considered in early and late planning stages.

"While a request was made to review the work of the commission, this was not considered necessary as that independent body had reported publicly, and for completeness it's work was referred to in the audit report.

"Potential conflict of interests are routinely considered and managed in all work undertaken in the audit office."

The ombudsman's office could not comment for reasons relating to confidentiality.