An investigation into what the prime minister's staff knew about an alleged rape of a former Liberal staffer has been paused over fears it could interfere with police.
Former ministerial adviser Brittany Higgins says she was raped by a former colleague inside Parliament House in March 2019.
Scott Morrison last month tasked Department of Prime Minister and Cabinet secretary Phil Gaetjens with investigating who in the prime minister's office knew about the allegation and when.
Mr Gaetjens told Senate estimates the commissioner advised him to pause his inquiry because it could compromise the criminal investigation.
He said he put his probe on hold on March 9 following advice from Mr Kershaw.
Mr Morrison, who initiated the investigation on February 17, didn't reveal the delay last week despite being asked in parliament about its progress.
He denied misleading the lower house after Labor leader Anthony Albanese pursued the issue in Question Time.
"I advised the house last week that he had not given me an update on when that report would be finalised and a time frame for that to be provided," the prime minister told parliament.
Australian Federal Police Commissioner Reece Kershaw issued a statement after giving evidence at odds with Mr Gaetjens at a separate hearing.
He confirmed telling the top public servant it was "strongly advisable" to hold off finalising interviews with staff until police could clarify any possible crossover.
"I support his decision to put on hold the process of finalising his inquiry," Mr Kershaw said.
"At this time, I support him not making any further comments on the process or content of his inquiry to avoid any risk of prejudicing the outcome of the criminal investigation."
He pledged to contact Mr Gaetjens to approve restarting the inquiry once it was determined there was no intersection between the investigations.
Earlier, Mr Kershaw said he had spoken with Mr Gaetjens about his particular concern about his inquiry.
When asked if the secretary's investigation could hamper police, Mr Kershaw said: "It may. It may."
"That's where I used the language around intersect with our investigation. Whilst I have the terms of reference we're not embedded in that inquiry nor would we want to."
Mr Gaetjens claimed he paused the inquiry for the benefit of Ms Higgins, sparking a furious backlash from Labor and Greens senators.
"Do not use her interests as a shield, Mr Gaetjens," opposition Senate leader Penny Wong said.
Mr Gaetjens also said he had not spoken to Ms Higgins during the inquiry out of respect for her privacy.
Green senator Sarah Hanson-Young took aim at the prime minister's department secretary.
"This is a cover-up. It stinks and now we have the AFP undermining the evidence you have given," she told the hearing.
Mr Kershaw said the allegation made by Ms Higgins was serious and being pursued by the AFP through its ACT policing arm.
Senate President Scott Ryan also came under fire for refusing to answer questions about the alleged assault.
Senator Ryan said he would not speak about the allegations which remain part of an active police investigation.