The former chief of staff for the senator Bruce Lehrmann and Brittany Higgins worked for said her "antenna was up" after asking him about a late night visit to Parliament House.
Fiona Brown had no reason to think he was lying and "accepted what everyone said" while asking questions about a weekend security breach.
"This was not an investigation," Ms Brown told the Federal Court on Monday.
It was almost two years before news reports of Ms Higgins' claim she was raped in Senator Linda Reynolds' office on March 23, 2019.
Lehrmann was not named in the reports in February 2021 but has sued Network Ten and journalist Lisa Wilkinson for defamation.
Ms Brown denied Ms Higgins told her in a meeting on March 26, 2019 she had been raped.
"She did not disclose that to me," she said.
Ms Brown was surprised and shocked two days later when Ms Higgins left another meeting with the "quite casual" remark that she remembered "him on top of me," she told the court.
Lehrmann's name was not used, Ms Brown said.
She said she had no reason to disbelieve Ms Higgins but did not understand what she had allegedly meant.
"I couldn't be making a criminal allegation against someone, Ms Higgins needed to expressly tell me that this was something she did not want."
She also denied Ms Higgins was hysterical and crying in the first meeting but said she gave her a tissue for a "watery eye" and a brochure for counselling through an employee assistance program.
She had earlier talked to Lehrmann, who left his ministerial pass with security on his way out afterwards.
"Bruce, I asked you to return it to me, I'm disappointed you've failed to follow a direct request," Ms Brown later texted him.
Ms Brown said she was curious and concerned about a potential security breach when she spoke to Lehrmann after learning he and Ms Higgins had attended after hours and apparently intoxicated before he left and she was found in a state of undress the next day.
"Did you suspect at that point that they had had sex?" Wilkinson's barrister Sue Chrysanthou SC asked.
"I couldn't rule it out and I couldn't rule it in," Ms Brown said.
Justice Michael Lee suggested Ms Brown had not formed the view Lehrmann was lying, but thought he was not being entirely candid.
"Yes my antenna was up," Ms Brown said.
The court's livestream was turned off for Ms Brown's evidence after mental health reports were presented to the court.
She returns on Tuesday.
Earlier, editorial consultant Peter Meakin, who worked with Network Ten on The Project broadcast, told the court more could have been done to probe her version of events.
Mr Meakin was "initially sceptical" of Ms Higgins' story but changed his mind after seeing the interview with Wilkinson.
He acknowledged material Parliament House provided to Ten contradicted Ms Higgins' claims about the alleged rape's aftermath.
It suggested Senator Reynolds and Ms Brown were supportive of her going to police and she could keep her job if she did.
The Project report said Ms Higgins was forced to choose between her career and making a police complaint, and presented the Parliament House culture as one in which her silence about the alleged incident was preferred.
Mr Meakin said the documents revealed a different narrative and it would have been "desirable" for Ten to double check.
Also on Monday, Queensland Liberal National Party MP Sam O'Connor said Ms Higgins told him of her alleged rape weeks after the incident.
"This super f***ed up thing happened a little while ago and I've just lost the fight," she wrote via text in April 2019.
In a phone conversation soon after those texts, Ms Higgins said she had been raped by a male Liberal staffer at Parliament House, he said.
Ms Higgins told him she didn't want to report the alleged incident to police fearing it would "define her" personally and professionally.
Lehrmann's trial in the ACT Supreme Court charged with raping Ms Higgins was derailed by juror misconduct.
Prosecutors did not seek a second trial, citing concerns for Ms Higgins' mental health.
He has been charged with allegedly raping another woman twice in Toowoomba in October 2021 and remains before Queensland courts.
He has not yet entered a plea but lawyers have indicated he denies that allegation.
1800 RESPECT (1800 737 732)
National Sexual Abuse and Redress Support Service 1800 211 028
