Microbiologist Michelle Adams said she was one of dozens of staff who had suffered bullying and harassment in recent years at the university and she believed it was an "ingrained culture" at the institution.
University vice-chancellor Nick Saunders said he did not believe bullying or harassment was a problem at the institution.
But he confirmed 57 complaints were investigated last year.
"To my knowledge bullying and harassment is not a major problem at the University of Newcastle in the context of an organisation that employs and teaches 35,000 staff and students," Professor Saunders said.
Dr Adams's case dates back to 2003 when she raised allegations of plagiarism against two fellow academics.
Following the allegation Dr Adams said she was treated like a "leper", frozen out of communication with colleagues, bullied in meetings and the hostility got so bad she was afraid to enter the staffroom.
In a statutory declaration to a Workers Compensation Commission conference last month she detailed being left off important emails, given an hour's notice by email to attend meetings at Ourimbah when she was at the Callaghan campus and feeling isolated.
"In the end I feared going to work and there were times when I would just break down and cry," she said.
"It has gone on for so long that it is hard to remember what life was like before all of this."
The University of Newcastle branch of the National Tertiary Education Union and Newcastle University Student Union launched a major anti-bullying campaign last year.
The unions said there was a "large volume" of cases in which staff and students reported ongoing bullying and harassment on campus.
Education union vice-president Rod Noble said in some cases staff had been forced to leave the university as a result.
"For some people there are fears of retribution and some are simply too afraid to speak out," Mr Noble said.
"People have left as they have felt that was the only way to resolve it."
Several former Newcastle University academics who spoke to The Herald confirmed a "culture of fear" and said if people spoke up they "risked their careers".
Professor Saunders said there was simply no evidence of a culture of bullying.
He said the university's complaints office dealt with 33 formal, or written, cases of harassment and bullying last year that were made by 27 people, with 22 cases upheld against 16 people.
Of them 17 cases related to bullying with 12 cases upheld against six people.
A further 24 informal complaints of harassment were made by 24 people and seven related to bullying. None of the seven informal complaints resulted in an investigation.
Professor Saunders said bullying and harassment was not tolerated and it was clearly against the university's code of conduct.
Punishment ranged from counselling to the university taking action for misconduct.
