Daniel James McCluskie, 45, was arrested at a home in Sydney's inner-west in July 2025 and now faces allegations involving three separate women.
He appeared on Tuesday before the District Court in Sydney, where he was arraigned on 16 charges including rape, choking and intimidation.
"Not guilty," he said after each charge was read to the court.
McCluskie was an advisor for the government-run Australian Digital Health Agency before his arrest.
The majority of charges against him relate to one woman and span from March 2021 to March 2023.
He is accused of raping that alleged victim nine times in Sydney and elsewhere in NSW, including one time when he allegedly inflicted actual bodily harm.
He also allegedly choked her twice, recorded an intimate image of her without her consent, and intimidated her on two occasions.
The other charges relate to alleged incidents with two other woman.
McCluskie is accused of raping one alleged victim in February 2021 and choking the other without her consent in March 2024.
Both of these charges allegedly occurred in Sydney's inner-west.
None of the alleged victims can be named for legal reasons.
A spokesperson for the federal agency said McCluskie had been engaged as a digital health advisor, but was no longer in that role.
The agency did not use his services and he did not contribute to or advise on any individual project or program, they told AAP.
His trial is expected to start in May.
1800 RESPECT (1800 737 732)
National Sexual Abuse and Redress Support Service 1800 211 028
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