The inquiry was established by the ACT government last year after allegations were made by the director of public prosecutions (DPP) and police forces about each other's conduct during the high-profile case.
Ms Higgins' former colleague Bruce Lehrmann faced an ACT Supreme Court trial in October, but it was derailed due to juror misconduct.
The charges against him were later dropped because of concerns about the impact a second trial would have on Ms Higgins' mental health.
Mr Lehrmann denies the allegation he raped Ms Higgins in Parliament House in 2019.
After the charges were dropped, it emerged ACT DPP Shane Drumgold had raised concerns about "political and police conduct" in the case.
But the police union hit back at the allegations and accused Mr Drumgold's office of compromising Mr Lehrmann's trial.
The territory government established the inquiry to ensure ACT criminal matters were prosecuted in a way that was robust, fair and respected the rights of those involved.
Former Queensland solicitor-general Walter Sofronoff was appointed head of the inquiry which will report back to the ACT government by June 30.
At an initial public hearing on Monday, Mr Sofronoff will outline the nature and scope of the inquiry which will examine the conduct of criminal justice agencies during Mr Lehrmann's trial.
The inquiry is expected to examine interactions between prosecutors and ACT Police regarding the charges against Mr Lehrmann as well as the decisions to go ahead with a first trial and then not proceed with a retrial.
It will also look at how the ACT Victims of Crime Commissioner - a support service for people who have experienced crime in the territory - assisted Ms Higgins.
