Vic Auditor-General complaint kept secret

A personal complaint from a staff member against the Victorian Auditor-General will remain a secret while the matter is investigated by a retired High Court judge.

The parliament has agreed to ask Kenneth Hayne QC to investigate John Doyle over what has been termed as a serious complaint.

But Greens leader Greg Barber was unhappy that MPs had to vote on whether to investigate the public watchdog without knowing why.

"We are concerned we are being asked to vote on a matter on which we have very little information," he told the parliament on Tuesday.

"We understand the matter could be serious, we understand the desire to protect those involved, however we are uncomfortable with that precedent that could be set."

The specific allegations have not been released and Mr Doyle will remain in office while the investigation is carried out.

Attorney-General Martin Pakula said it was Mr Doyle's choice not to step down during Mr Hayne's investigation, announced on Monday.

"It is very clear under the constitution that the Auditor-General has very strong protections in regards to the independence of that office, so he has indicated that he will continue to do his job during that investigation," Mr Pakula said.

"The Auditor-General's independence is protected very jealously, as it ought to be, by the constitution."

Mr Pakula said he did not know the details of the complaint against Mr Doyle.

The Public Accounts and Estimates Committee met on Monday to decide how to investigate the personal grievance complaint, which was lodged on August 12.

Mr Hayne will investigate the complaint and whether Mr Doyle should be removed from office.

"I will be fully co-operating with the investigation, but will not be making any public comment while proceedings are being undertaken," Mr Doyle has said in a statement.

The committee will report to the parliament before October 20.