Brittany Higgins says she was sexually assaulted by a male colleague inside Parliament House in 2019.
Scott Morrison claims his office did not find out about the alleged rape until last week and he was not informed until Monday.
But records show a text message exchange between Ms Higgins and a fellow Liberal staffer within a fortnight of the incident.
In the message, the Liberal staffer said he had spoken directly with a member of Mr Morrison's staff.
"Spoke to PMO. He was mortified to hear about it and how things have been handled," he said.
"He's going to discuss with COS — no one else. I flagged need for councillor (sic) and desire to be closer to home during election."
PMO refers to the prime minister's office and COS is shorthand for chief of staff.
The prime minister is standing by his timeline, despite Ms Higgins saying at least three of his staff had prior knowledge of the incident.
While the messages appear to confirm her account, Mr Morrison wants the nation's top public servant to review communication records.
"If there was anything different here, I would like to know," he told reporters in Sydney on Friday.
"I want to know and that is why I have asked the secretary of my department to actually test that advice that I received."
Mr Morrison denied he had misled the public and maintains he is horrified by the allegations.
"I have sought to be as open and honest as I can be about this matter. I have told you everything I know about this matter. I will continue to," he said.
Labor leader Anthony Albanese said the text messages completely contradicted Mr Morrison's claim that his office wasn't informed until last week.
"It's just incomprehensible that the prime minister's office, given a reported sexual assault had occurred 50 metres from his office, wouldn't have then had a discussion about handling the issue," he told the ABC.
It just doesn't stack up.
Mr Albanese said Ms Higgins deserved straight answers about who knew what and when.
"I believe Brittany Higgins when it comes to the incident and tragedy."
Home Affairs Minister Peter Dutton said the prime minister's public statements on the timeline were based on advice from his staff.
"If he has been misled then that is a different level for him to deal with," Mr Dutton told Nine.
"But on the advice he has received during the week, and as he said in parliament, that's the facts as he knows them. To be reasonable, he can only report the facts as he's advised by his staff."
The Project has separately approached the PMO for comment.
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