Demographer Liz Allen appeared before a parliamentary inquiry in August 2025, where she blew the whistle on bullying and hostile behaviour from the ANU Council.
She has received an undisclosed payout.
In a statement on Tuesday, the university commended Dr Allen for "courageously" speaking out about misconduct by senior leadership, and failures of governance.
"Publications were made about Dr Allen that were false and unjustified," it reads.
"These publications should not have occurred and the University unreservedly apologises for the university's part in these events, for the maladministration of several processes, and for its indefensible treatment of her.
"The university accepts that it has failed Dr Allen and that these failings have caused her considerable harm. The university unreservedly apologises to Dr Allen for all of its failings and the harm it has caused her."
Dr Allen, a former staff-elected member of the council, said she had experienced a miscarriage due to the stress and treatment she experienced.
In a statement posted to social media, the academic said she was "pleased" with the resolution with ANU.
"I look forward to helping the university rebuild trust and helping to ensure that what happened to me is not the experience of future whistleblowers," Dr Allen said.
"I would like to thank ... my friends in parliament and academia, and my husband and family whose unwavering support sustained me."
Ms Bishop resigned this year as chancellor following months of mounting pressure from staff and students.
Then vice-chancellor Genevieve Bell resigned in September following intense scrutiny amid disquiet over staff redundancies.
ACT senator David Pocock said whistleblowers needed greater protections.
"Whistleblowers, like Dr Liz Allen, show enormous courage and play a critical role exposing wrongdoing at the highest levels," he wrote on X.
"I welcome this apology and settlement and seeing both Dr Allen and the new leadership at the ANU move forward in a brighter chapter for one of our most loved institutions."
