Lawyers representing the academics argued in Quebec Superior Court on Wednesday the interview with a subject known under the pseudonym "Jimmy" should be kept confidential.
The lawyers say Magnotta participated in the study as part of a survey of sex workers under the condition his interview would remain confidential. Magnotta's lawyers, who have supported the researchers' motion, filed an affidavit confirming that later Wednesday.
Montreal police want a copy of the interview for evidence they're still gathering against Magnotta.
The 30-year-old is charged with first-degree murder in the slaying and dismemberment of Chinese engineering student Jun Lin.
Police came to know about the interview after a research assistant, Adam McLeod, told them about it following Magnotta's arrest last year. McLeod told authorities "Jimmy" was in fact Magnotta.
Peter Jacobsen, a lawyer representing the criminologists Dr. Colette Parent and Dr. Christine Bruckert, said he's not sure McLeod even realized he was breaking confidentiality when he called police. He suggested McLeod may have just been caught up in the media hype surrounding the case.
The fact he didn't think of it is problematic, Jacobsen said. Confidentiality is paramount in academia when dealing with sensitive topics.
"The promise of confidentiality must be upheld otherwise this type of research into the work of vulnerable and stigmatized groups like sex workers would not be possible," he said.
"They didn't even want his own handwriting on the document for fear it could be used to identify him," Jacobsen added.
"There was a serious and strong effort made to keep the material confidential."
If they can't promise confidentiality, sources will dry up, Jacobsen said.
Jacobsen doesn't believe the interview would even be relevant to the criminal case.
He said a forensic psychiatrist examined the study interview and found it would be of little use in a not-criminally responsible defence.
Crown prosecutor Alexandre Boucher conceded there might not be much to the material, but he urged Justice Sophie Bourque to look at the March 2007 interview before deciding on the petitioners' request.
The petitioners want to have the warrant quashed and the 68-page transcript and audio interview returned.
Boucher said the document should at least be looked at, since McLeod thought it was important enough for him to contact police.
"I don't know what's in the material, maybe there's nothing there," Boucher said.
"But if there is something, you'll be able to see and decide for yourself."
He noted that perhaps Bourque would prefer not to rule on the matter and leave it up to the trial judge.
The material will remain sealed while the legal debate plays out.
Bourque said Wednesday she hasn't decided whether she'll unseal the document. Jacobsen said the two professors do not want her to look at the material if isn't absolutely necessary.
The case returns to a Montreal courtroom on Thursday.
Jacobsen says a promise was made to Magnotta that the interview, conducted during a study on sex-trade workers and their clients, would remain confidential.
He says great lengths were taken to protect Magnotta's identity. His real name doesn't appear anywhere and he didn't sign the confidentiality agreement in case his handwriting was recognized.
"It's important that their research be kept confidential because if it's not ... people will not speak to them in the future about these issues," Jacobsen said outside the courtroom.
Jacobsen also cast doubt on the relevance of a 2007 interview, given the fact Magnotta's alleged crimes occurred in 2012.
Magnotta's preliminary hearing, which will determine whether he'll have to stand trial on the murder charge, resumes Monday.
Evidence presented at the hearing is subject to a publication ban.
Magnotta has pleaded not guilty to five charges and opted for a jury trial.
His lawyers are also arguing separately before Quebec Superior Court for more money from legal aid to pay for a pre-trial psychiatric evaluation.
Magnotta's lawyer has not said what type of defence he plans to present.
Also on Wednesday, a letter from Magnotta's psychiatrist, filed during a previous conviction in 2005 for fraud, was made public.
The letter said that Magnotta had suffered from paranoid schizophrenia since at least 2000 and was hospitalized several times, though his doctor said he didn't always take his medication.
The document was released after several media outlets fought for it to be made public.