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A statement from the university said vice-chancellor Harlene Hayne criticised the "reporting, accuracy and responsibility of TVNZ as a public broadcaster''.
The programme included excerpts from letters between senior university staff members released under the Official Information Act to one of the students, who called herself "Michaela'' in the programme.
Michaela said she was assaulted after signing up for a blind date organised by Critic Te Arohi student magazine.
A sentence from one email read on Sunday said if the matter had led to a rape complaint "it would not have been a good look for the University of Otago'', and featured the former university student saying the emails revealed "damage control'' on the part of the university.
The university statement said the emails featured in the programme were about the dating column.
They were taken out of context, and the idea the university was more concerned about its reputation might potentially deter students from complaining.
Prof Hayne said there was no link between the references to reputation and what the university actually did to try to help Michaela.
"To draw that link is irresponsible, unfair and an example of inaccurate, selective reporting.
"We strongly refute this allegation, and we stand by our handling of the cases that Sunday focused on, and the sensitivity and fairness in the way we investigate complaints, and ultimately support our students.''
The university had a comprehensive, student-centred approach to reports of sexual assault, where confidentiality was paramount, the university said.
College staff were trained to provide initial support to complainants, and to refer them to in-house services, including sexual violence drop-in centre Te Whare Tawharau, or publicly available ones, such as the police.
Sunday executive producer Jane Skinner said Sunday stood by its report and the women had the right to share their stories.
Of the email in question, only one paragraph related to the Critic column and the rest related to Michaela's case.
"The emails quoted in Sunday's story were central to one student's experience.
"This student upon accessing these emails strongly felt the university had prioritised their reputation over her wellbeing.''
Michaela said yesterday the story was balanced and well-researched and she stood behind what had been reported.
A spokeswoman said the university was reserving all its options including its right to take legal action against TVNZ.
Another former student, Olivia Montgomery, claimed on Sunday she was not taken seriously by her hall of residence Knox College when she reported instances of sexual harassment, and she said she had also tried unsuccessfully to raise concerns with the university.
Her lack of confidence in Knox College led to her not making a formal complaint when she was allegedly raped by a former Knox resident.
Ms Montgomery said yesterday she felt the university was "gaslighting'' victims by saying things had changed.
"The reason why you aren't hearing women who are currently [at Knox] is because they are afraid. And these responses from the university are hindering rather than helping,'' she said.
"Women continue to be assaulted in Dunedin every weekend,'' she said.
"I am yet to see a single story where the perpetrator of assault has been held accountable.
"Merely campaigns to protect the university as more and more women speak up.''
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