Brittany Higgins alleges she was sexually assaulted by a male colleague after a night out in 2019.
Morrison has expressed frustration he was not made aware of the allegations until this week.
But Higgins says she was contacted by a senior member of Morrison’s staff earlier this year after similar issues were raised in a Four Corners report.
Asked about this telephone call, Morrison questioned her memory of events.
“That is not the recollection of the records of my staff on that matter – it’s just not – so I can’t really speak more to it than that,” he told reporters in Canberra.
“I understand that over time, particularly in situations like this, that information can become confused over time about who makes contact and things like that. I accept that, I make no judgments about that.”
The prime minister sidestepped a follow-up question about whether Higgins was mistaken in her recount.
“I can’t comment on it because I wasn’t a party to either of the conversations,” he said.
Earlier, he apologised over the initial handling of the allegations.
Higgins welcomed his apology but said it should not have taken her story, or that of other survivors, to take action on workplace sexual harassment, assault or bullying.
She said the announcement of an investigation into the culture in Parliament House was also a welcome first step, but long overdue.
“There needs to be an independent reporting mechanism for staff where they can confidently and safely make complaints – similar to processes in many other workplaces in Australia and abroad,” she said.
“Political parties also need to conduct their own internal reviews and establish formal accountability processes.”
Higgins decided not to pursue a police complaint at the time of her alleged rape because she was worried about losing her job
She has since resigned and plans to reinstate the police complaint.
She also intends to initiate a formal complaint with the Department of Finance, which handles work-related complaints from ministerial staff.
“Everyone should feel safe to report sexual assault without fear of losing their job. These incidents shouldn’t have to play out in the media for change to happen,” she said.
Higgins is the third Liberal staffer to allege she was sexually assaulted by men in the party.
Defence Minister Linda Reynolds, who employed Higgins at the time of the alleged rape, has apologised unreservedly for her handling of the incident.
Reynolds said she deeply regrets speaking with Higgins in the place of the alleged attack, and at all times her intention was to empower the young woman.
The prime minister’s office was involved in managing the incident from the beginning.
But despite the engagement of at least two of his staff, Morrison said he was not made aware until 24 hours ago.
He denied there was a “don’t ask, don’t tell” policy in his office.
“I can assure you there is no such culture and I’m not happy about the fact it was not brought to my attention,” Mr Morrison said.
He has asked Curtin MP Celia Hammond, a former university vice chancellor, to work with party whips and MPs to improve workplace standards and protect staff.
Department of Prime Minister and Cabinet deputy secretary Stephanie Foster will also review processes for workplace allegations, with an automatic reporting obligation to department officials to be established.
The Liberal Party recently released a national code of conduct for handling complaints and Labor is in the final stages of adopting an updated version of its existing harassment processes and policies.
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