Victoria's auditor-general John Doyle has resigned a month after an official complaint was made against him by a female staff member.

Mr Doyle is under investigation by a state parliamentary committee over the matter, which has been led by recently retired High Court justice Kenneth Hayne.

At the time the complaint was made, Mr Doyle said he would continue in the role as auditor-general, but today tendered his resignation to the Parliament.

In a statement, the Public Accounts and Estimates Committee said it was still required to finish the investigation into Mr Doyle and would report back to Parliament by October 20.

The exact nature of the complaint is not known but Mr Doyle has previously called it "a personal grievance matter".

Acting Premier Jactina Allan said work to find a replacement for Mr Doyle would start immediately.

"The Public Accounts and Estimates Committee will be progressing the process for both an interim replacement, an acting replacement very shortly, and also in the longer term starting the process to replace the auditor-general," she said.

The auditor-general is an independent officer of the Victorian Parliament appointed to examine the management and use of resources within the public sector.

Mr Doyle was appointed to the role in 2013, having previously worked in Western Australia and Canada.