Cooper's colleague, Associate Professor Jeremy Austin, was serving as acting director of ACAD in the interim.
An external consultant had been brought in to interview past and present students.
One of them, Dr Nic Rawlence, now director of the University of Otago's Palaeogenetics Laboratory, said in his submission, provided to the Herald, that he had left ACAD with "literally no confidence" and severe health problems.
"In many ways it has taken me six years to recover from ACAD, while in some I still haven't," he said.
"While I'm now confident in my writing and public speaking, I'm still left with health issues, (which are flooding back writing this), from my time at ACAD."
Cooper, named South Australian Scientist of the Year in 2016, has played an influential role in the field of ancient DNA, in an academic career that has taken him from Victoria University, to the Smithsonian Institution, and the University of Oxford.
He moved to the University of Adelaide in 2005 and later set up ACAD there, helping change what we know about the ancient origins of species, including kiwi.
Attempts by the Herald to reach him by phone and email were unsuccessful.
Last week, the New Zealand Association of Scientists released a statement urging institutions to take allegations of bullying seriously.
"Most importantly, open discussions on expected behaviour in science need to be facilitated," its president, Heide Friedrich, said.
New Zealand has lacked a clear definition of bullying that matched formal definitions of "harassment".
But the Royal Society Te Apārangi's new Code of Professional Standards now called for members to demonstrate ethical behaviour and professional standards by "avoid[ing] falsely, vexatiously or maliciously impugning the reputations of colleagues or otherwise compromising or denigrating them in order to achieve commercial, professional or personal advantages".
