Scott Morrison has conceded his defence minister should have told him about an alleged rape in Parliament House without identifying the woman involved.
Embattled frontbencher Linda Reynolds is on medical leave after coming under intense pressure over her handling of former Liberal staffer Brittany Higgins' sexual assault allegation.
Ms Higgins says she was raped by a fellow ministerial adviser in Senator Reynolds office in 2019.
Senator Reynolds has repeatedly said she didn't tell the prime minister out of respect for Ms Higgins' privacy.
Mr Morrison said the minister should have raised the rape allegation with him without identifying the people involved.
"I wish she had, but she did not," he told parliament on Thursday.
"I would hope that in the future, if people wish to protect the privacy of any individual, they could raise these matters in an anonymised way."
Australian Federal Police Commissioner Reece Kershaw has written to the prime minister saying all criminal conduct should be reported without delay.
"I cannot state strongly enough the importance of timely referrals of allegations of criminal conduct," Mr Kershaw said.
He said the failure to report criminal behaviour or allowing allegations to be aired in the media risked prejudicing police investigations.
"By not adhering to this process, there is a real risk that any alternative actions by individuals may lead to obstructing, preventing, perverting or defeating the course of justice or administration of the law."
Mr Morrison said Senator Reynolds followed the correct process by meeting with police about the incident.
Ms Higgins withdrew the complaint in the weeks after the alleged assault, fearing her job was at stake if she proceeded, before reinstating it on Wednesday.
While apologising for the level of support afforded to the former media adviser, Mr Morrison also noted Senator Reynolds did offer her help.
Home Affairs Minister Peter Dutton knew about the matter four days before the prime minister earlier this month, but didn't tell him out of fear he could compromise a potential police investigation.
Ms Higgins spoke to police on February 5, with the AFP then informing Mr Dutton six days after that because it was a politically sensitive investigation.
The minister decided it was an operational matter for police.
"I took a decision that I wasn't going to disclose that to the prime minister," Mr Dutton told reporters in Canberra on Thursday.
"That was the right decision."
Mr Dutton told Mr Morrison's office about the rape allegations on February 12 after media enquiries.
"I wasn't provided with the 'she said, he said' details of the allegations. It was at a higher level and that's the basis on which we provided information," he said.
Three other women have alleged they were assaulted by the man since Ms Higgins came forward.
He was sacked after the incident because of a security breach on the night of the alleged rape.
Mr Morrison has consistently said his office first knew of the allegation on February 12, but staff took almost three days to notify him.
Australian Associated Press
