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AUT's Dean of the Faculty of Health and Environmental Sciences Max Abbott has resigned with immediate effect.
In a statement, AUT vice chancellor Derek McCormack said he accepted Abbott's resignation on Friday.
Abbott would continue as a professor at the university.
His resignation comes after Dr Marisa Paterson, director of the Centre for Gambling Research at Canberra's Australian National University (ANU), laid a complaint against Abbott last August.
The complaint detailed allegations of "prolonged and persistent stalking, sexual harassment, physical harassment and bullying" by Abbott over a two-year period.
McCormack said it was essential that all staff and students have full confidence in its approaches to preventing and dealing with harassment.
"We want to be certain we are are a place where all of our people feel welcome, safe and able to succeed - and able to raise concerns if that's not the case."