Ms Higgins told Wilkinson and Ten producer Angus Lewellyn she had lost all data on her mobile but still retained a few messages and photographs she handed over as evidence that she was allegedly sexually assaulted by Bruce Lehrmann.
Wilkinson was asked about this meeting, which took place in a Sydney hotel on January 27, 2021, in the Federal Court during defamation proceedings brought by Lehrmann.
She described a claim by Ms Higgins that the federal government could remotely wipe phones as "curious" and "strange".
"I was trying to get to the bottom of the phone situation, so alarm bells were ringing for me," she said under cross-examination by Lehrmann's barrister, Matthew Richardson SC on Thursday.
She denied the barrister's suggestion this should have made her question Ms Higgin's reliability, instead saying the claim made her see the alleged rape survivor as a "very scared young woman".
Lehrmann's lawyer Matthew Richardson has questioned TV presenter Lisa Wilkinson. (Bianca De Marchi/AAP PHOTOS)
Lehrmann is suing Network Ten and Wilkinson for defamation over a February 2021 report on The Project that aired Ms Higgins' claims.
In the interview, Ms Higgins said the alleged rape occurred in the office of her then-boss Senator Linda Reynolds in the early hours of March 2019.
Lehrmann has always denied any sexual contact between himself and Ms Higgins, and is chasing Network Ten and Wilkinson in the Federal Court for damages.
Wilkinson said because of the sensitive nature of sexual assault, Mr Lewellyn had been assigned as the only person from Ten to have contact with Ms Higgins during the preparatory stages.
She said she had spoken to the producer about the phone issue but was told it should be ignored as it raised "unanswerable questions" and weakened rather than strengthened Ms Higgins' allegations.
She also escalated her concerns to two other senior members in the team, Wilkinson told the court.
"I was told it had been further investigated and it was now a non-issue," she said.
The journalist also rejected propositions by Mr Richardson that an award speech after The Project won a silver Logie for the Higgins report was "reckless and ill-advised".
The speech was made eight days before Lehrmann's criminal trial over the alleged rape was due to begin and resulted in the proceedings being postponed because of fears her comments could have influenced potential jury members.
"You put your pride and your ego ahead of my client's right to a fair trial when you gave that speech," Mr Richardson said.
"I completely disagree," Wilkinson replied.
Lehrmann was charged in August 2021 over the alleged rape, but his criminal trial in the ACT Supreme Court was derailed by juror misconduct.
Prosecutors did not seek a second trial, citing concerns for Ms Higgins' mental health.
Lehrmann is also before Queensland courts accused of raping another woman twice in Toowoomba in October 2021.
He has not entered a plea, but his lawyers have indicated he denies the charges.
1800 RESPECT (1800 737 732)
National Sexual Abuse and Redress Support Service 1800 211 028