Federal Police Commissioner Reece Kershaw has confirmed he was behind the advice to halt an administrative inquiry into Brittany Higgins' rape allegation to avoid risking prejudicing a criminal investigation.
Clarifying contradictory evidence heard in Senate estimates hearings on Monday morning, Mr Kershaw said he reviewed the statement of top official Phil Gaetjens.
"I confirm I informed Mr Gaetjens on 9 March it was strongly advisable to hold off finalising the records of interviews with staff until the AFP could clarify whether the criminal investigation into Ms Higgins' sexual assault allegations may traverse any issues covered by the administrative process he was undertaking," Mr Kershaw said in the statement.
"I support his decision to put on hold the process of finalising his inquiry."
Mr Kershaw said that he supported the decision to not make further comments on the process or content of his inquiry.
The AFP would advise Mr Gaetjens when it was safe to resume his inquiry, he added.
Prime Minister Scott Morrison was aware the inquiry had been halted for more than a week when he told parliament that questions could be asked about it at Senate estimates.
Mr Gaetjens told an estimates hearing his investigation into what the Prime Minister's staff knew of the allegation was paused "for the benefit of Ms Higgins" on the advice of Mr Kershaw.
Labor and Greens senators reacted with disgust at the assertions and accused the government of a "cover-up".
Reading a short statement confirming the investigation was put on hold, Mr Gaetjens said the decision was made on Tuesday, March 9, the same day Mr Kershaw had a call with Mr Gaetjens. The Prime Minister was informed of the decision later that day.
Labor seized on the revelations during question time on Monday, accusing Mr Morrison of misleading Parliament about his knowledge of the status of the Gaetjens inquiry.
Mr Morrison last Thursday, March 18, told parliament that "those inquiries were being made", when asked if his chief of staff and principal private secretary had been interviewed about their knowledge of Ms Higgins' allegations.
Mr Gaetjens' inquiry had at that point been on hold for nine days.
Mr Morrison rejected Labor's accusations, as he insisted Mr Gaetjens' review was being conducted at "arm's length".
"I have been very clear with this House," he said.
Mr Gaetjens told one estimates hearing the commissioner told him to ensure there was "no intersection with the criminal investigation" and that he was concerned about witness statements produced by the Gaetjens investigation.
"Because of AFP commissioners' advice I would not be completing the documentation, as per the commissioner's advice that there is no intersection," Mr Gaetjens told the hearing on Monday.
Mr Kershaw told another estimates hearing on Monday morning that it was a matter for Mr Gaetjens and he did not have access to those statements.
When the commissioner was asked directly if he asked for the inquiry to be paused or altered, Mr Kershaw replied, "No".
Labor's Katy Gallagher accused the Prime Minister of sending his right-hand man into the hearing "to answer questions about the inquiry and all the while knowing you wouldn't".
"The Department of the Senate can't answer questions. The Department of Parliamentary Services can't answer questions. You can't answer questions either," Senator Gallagher said.
Mr Gaetjens appeared at a different hearing after lunch on March 9, and said he was waiting on witnesses for the investigation, but did not tell the hearing that work on it was indefinitely halted.
"I wasn't asked," Mr Gaetjens said on Monday.
Concurrent reviews of parliamentary culture by Sex Discrimination Commissioner Kate Jenkins and senior official Stephanie Foster were not halted, the government confirmed.
Multiple security officials in parliament had seen the CCTV footage of the night of the alleged rape, the hearing heard.
Parliamentary Services department head Rob Stefanic confirmed the access but said it was a limited number of individuals. He could not confirm if that included political staffers or anyone from the Prime Minister's office.
Ms Higgins has claimed the Prime Minister's office was "negatively backgrounding" reporters to smear her partner, but officials from the Prime Minister's department were unable to answer questions relating those claims on Monday.
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