Fiona Brown is suing the Commonwealth for damages, saying the Morrison government gagged her from responding to accusations about her handling of Ms Higgins' claims.
Ms Brown held a leadership role in the then-prime minister's office when the Higgins scandal erupted publicly in 2021.
She earlier served as chief of staff to then-senator Linda Reynolds in 2019 when Ms Higgins said a fellow Reynolds staffer raped her in Parliament House.
Ms Brown's dispute returns to the Federal Court in Sydney for a case management hearing on Monday.
In a 106-page court filing, she alleges she was sidelined from leadership meetings and the then-prime minister refused to talk to her after the scandal broke in early 2021.
Labor later used question time to probe Mr Morrison about claims Ms Brown had not supported Ms Higgins, leading the prime minister to say: "I have had these conversations with the member of staff."
"I have discussed with her those matters and the support provided to her at the time in the messages that were sent to her," he told parliament.
Mr Morrison subsequently spoke briefly with Ms Brown for the first and only time, she claims.
"We've spoken, haven't we?" he allegedly said.
The filing says a "bewildered" Ms Brown responded "yes" and Mr Morrison walked off.
"(Ms Brown) complained that she felt frightened, intimidated and distressed by Prime Minister Morrison," the filing said.
The former aide also accuses Mr Morrison and his top-level advisers of stopping her from personally responding to allegedly false allegations made by Ms Higgins.
Ms Higgins' appearance on Network Ten's The Project included identifying Ms Brown by name and accusing her of misconduct for the mishandling of the rape, the documents say.
Before the show, Ms Brown had been contacted by a producer for comment but was allegedly told by Mr Morrison's chief of staff not to respond.
One of the key pieces of evidence contradicting Ms Higgins' claim was a text she allegedly sent to Ms Brown thanking her for her support immediately after the rape.
But the advisers repeatedly told Ms Brown not to respond to any media inquiries, saying to do so would "kick the story along", the documents say.
She claims this conduct was in breach of the Fair Work Act by causing her psychological injury to the point she attempted suicide.
The Commonwealth is yet to file its defence.
A four-week hearing is set to begin in March 2027.
In an earlier Federal Court case, Federal Court Justice Michael Lee found Ms Brown had shown compassion and integrity in her handling of Ms Higgins' complaint but she had been unfairly "vilified as an unfeeling apparatchik" seeking to cover up a crime.
Justice Lee's finding that on the balance of probabilities Bruce Lehrmann raped Ms Higgins was confirmed by the full Federal Court in December.
Lehrmann's criminal trial was derailed due to juror misconduct.
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